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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 3-131535304-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=131535304&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 131535304,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_153429.2",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1565G>A",
"hgvs_p": "p.Ser522Asn",
"transcript": "NM_130808.3",
"protein_id": "NP_570720.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 557,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000429747.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130808.3"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1565G>A",
"hgvs_p": "p.Ser522Asn",
"transcript": "ENST00000429747.6",
"protein_id": "ENSP00000411904.1",
"transcript_support_level": 1,
"aa_start": 522,
"aa_end": null,
"aa_length": 557,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_130808.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000429747.6"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Ser540Asn",
"transcript": "ENST00000512332.5",
"protein_id": "ENSP00000424853.1",
"transcript_support_level": 1,
"aa_start": 540,
"aa_end": null,
"aa_length": 575,
"cds_start": 1619,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512332.5"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1565G>A",
"hgvs_p": "p.Ser522Asn",
"transcript": "ENST00000511604.5",
"protein_id": "ENSP00000423811.1",
"transcript_support_level": 1,
"aa_start": 522,
"aa_end": null,
"aa_length": 557,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000511604.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "n.563G>A",
"hgvs_p": null,
"transcript": "ENST00000514439.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000514439.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Ser540Asn",
"transcript": "NM_001289112.2",
"protein_id": "NP_001276041.1",
"transcript_support_level": null,
"aa_start": 540,
"aa_end": null,
"aa_length": 575,
"cds_start": 1619,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001289112.2"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Ser540Asn",
"transcript": "NM_153429.2",
"protein_id": "NP_702907.1",
"transcript_support_level": null,
"aa_start": 540,
"aa_end": null,
"aa_length": 575,
"cds_start": 1619,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153429.2"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Ser540Asn",
"transcript": "ENST00000502818.5",
"protein_id": "ENSP00000421646.1",
"transcript_support_level": 5,
"aa_start": 540,
"aa_end": null,
"aa_length": 575,
"cds_start": 1619,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502818.5"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Ser540Asn",
"transcript": "ENST00000617767.5",
"protein_id": "ENSP00000478878.1",
"transcript_support_level": 2,
"aa_start": 540,
"aa_end": null,
"aa_length": 575,
"cds_start": 1619,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000617767.5"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1565G>A",
"hgvs_p": "p.Ser522Asn",
"transcript": "ENST00000512055.5",
"protein_id": "ENSP00000421705.1",
"transcript_support_level": 2,
"aa_start": 522,
"aa_end": null,
"aa_length": 557,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512055.5"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1565G>A",
"hgvs_p": "p.Ser522Asn",
"transcript": "ENST00000886213.1",
"protein_id": "ENSP00000556272.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 557,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886213.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1565G>A",
"hgvs_p": "p.Ser522Asn",
"transcript": "ENST00000933672.1",
"protein_id": "ENSP00000603731.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 557,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933672.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1565G>A",
"hgvs_p": "p.Ser522Asn",
"transcript": "ENST00000943028.1",
"protein_id": "ENSP00000613087.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 557,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943028.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1565G>A",
"hgvs_p": "p.Ser522Asn",
"transcript": "ENST00000943029.1",
"protein_id": "ENSP00000613088.1",
"transcript_support_level": null,
"aa_start": 522,
"aa_end": null,
"aa_length": 557,
"cds_start": 1565,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943029.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1559G>A",
"hgvs_p": "p.Ser520Asn",
"transcript": "ENST00000943030.1",
"protein_id": "ENSP00000613089.1",
"transcript_support_level": null,
"aa_start": 520,
"aa_end": null,
"aa_length": 555,
"cds_start": 1559,
"cds_end": null,
"cds_length": 1668,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943030.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1481G>A",
"hgvs_p": "p.Ser494Asn",
"transcript": "ENST00000886212.1",
"protein_id": "ENSP00000556271.1",
"transcript_support_level": null,
"aa_start": 494,
"aa_end": null,
"aa_length": 529,
"cds_start": 1481,
"cds_end": null,
"cds_length": 1590,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886212.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1466G>A",
"hgvs_p": "p.Ser489Asn",
"transcript": "ENST00000943031.1",
"protein_id": "ENSP00000613090.1",
"transcript_support_level": null,
"aa_start": 489,
"aa_end": null,
"aa_length": 524,
"cds_start": 1466,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943031.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1379G>A",
"hgvs_p": "p.Ser460Asn",
"transcript": "ENST00000943032.1",
"protein_id": "ENSP00000613091.1",
"transcript_support_level": null,
"aa_start": 460,
"aa_end": null,
"aa_length": 495,
"cds_start": 1379,
"cds_end": null,
"cds_length": 1488,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943032.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1376G>A",
"hgvs_p": "p.Ser459Asn",
"transcript": "ENST00000933671.1",
"protein_id": "ENSP00000603730.1",
"transcript_support_level": null,
"aa_start": 459,
"aa_end": null,
"aa_length": 494,
"cds_start": 1376,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933671.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1226G>A",
"hgvs_p": "p.Ser409Asn",
"transcript": "NM_001388326.1",
"protein_id": "NP_001375255.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 444,
"cds_start": 1226,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001388326.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1226G>A",
"hgvs_p": "p.Ser409Asn",
"transcript": "NM_001388327.1",
"protein_id": "NP_001375256.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 444,
"cds_start": 1226,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001388327.1"
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CPNE4",
"gene_hgnc_id": 2317,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Ser544Asn",
"transcript": "XM_047447422.1",
"protein_id": "XP_047303378.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 579,
"cds_start": 1631,
"cds_end": null,
"cds_length": 1740,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
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{
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{
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{
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{
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{
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{
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],
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},
{
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"gene_symbol": "ENSG00000306539",
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},
{
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],
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"gene_symbol": "ENSG00000306539",
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"transcript": "ENST00000819264.1",
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"biotype": "pseudogene",
"feature": "ENST00000819264.1"
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],
"gene_symbol": "CPNE4",
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"dbsnp": "rs561689852",
"frequency_reference_population": 0.000005577556,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000410605,
"gnomad_genomes_af": 0.0000196915,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.14030721783638,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.079,
"revel_prediction": "Benign",
"alphamissense_score": 0.2358,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.853,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_153429.2",
"gene_symbol": "CPNE4",
"hgnc_id": 2317,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Ser540Asn"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000819262.1",
"gene_symbol": "ENSG00000306539",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.645C>T",
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}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}