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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: 3-3040078-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=3040078&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 3040078,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_175607.3",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "NM_175607.3",
"protein_id": "NP_783200.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000418658.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_175607.3"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "ENST00000418658.6",
"protein_id": "ENSP00000396010.1",
"transcript_support_level": 5,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_175607.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000418658.6"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.1221T>C",
"hgvs_p": "p.Tyr407Tyr",
"transcript": "ENST00000397459.6",
"protein_id": "ENSP00000380600.2",
"transcript_support_level": 1,
"aa_start": 407,
"aa_end": null,
"aa_length": 698,
"cds_start": 1221,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397459.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "n.455T>C",
"hgvs_p": null,
"transcript": "ENST00000484686.1",
"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": "ENST00000484686.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "NM_001206955.2",
"protein_id": "NP_001193884.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001206955.2"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "NM_001350095.2",
"protein_id": "NP_001337024.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001350095.2"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "ENST00000397461.5",
"protein_id": "ENSP00000380602.1",
"transcript_support_level": 5,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397461.5"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "ENST00000427331.5",
"protein_id": "ENSP00000413642.1",
"transcript_support_level": 5,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000427331.5"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "ENST00000968521.1",
"protein_id": "ENSP00000638580.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968521.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2043T>C",
"hgvs_p": "p.Tyr681Tyr",
"transcript": "ENST00000968522.1",
"protein_id": "ENSP00000638581.1",
"transcript_support_level": null,
"aa_start": 681,
"aa_end": null,
"aa_length": 972,
"cds_start": 2043,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968522.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.1221T>C",
"hgvs_p": "p.Tyr407Tyr",
"transcript": "NM_175613.3",
"protein_id": "NP_783302.1",
"transcript_support_level": null,
"aa_start": 407,
"aa_end": null,
"aa_length": 698,
"cds_start": 1221,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_175613.3"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.1218T>C",
"hgvs_p": "p.Tyr406Tyr",
"transcript": "NM_001206956.2",
"protein_id": "NP_001193885.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 697,
"cds_start": 1218,
"cds_end": null,
"cds_length": 2094,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001206956.2"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "XM_011533425.4",
"protein_id": "XP_011531727.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533425.4"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "XM_011533427.3",
"protein_id": "XP_011531729.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533427.3"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "XM_011533428.3",
"protein_id": "XP_011531730.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533428.3"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "XM_011533429.3",
"protein_id": "XP_011531731.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533429.3"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "XM_011533430.3",
"protein_id": "XP_011531732.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533430.3"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "XM_017005782.2",
"protein_id": "XP_016861271.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017005782.2"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "XM_017005783.2",
"protein_id": "XP_016861272.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017005783.2"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "XM_017005784.3",
"protein_id": "XP_016861273.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017005784.3"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "XM_047447516.1",
"protein_id": "XP_047303472.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
"cds_length": 3081,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047447516.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTN4",
"gene_hgnc_id": 2174,
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr",
"transcript": "XM_047447517.1",
"protein_id": "XP_047303473.1",
"transcript_support_level": null,
"aa_start": 735,
"aa_end": null,
"aa_length": 1026,
"cds_start": 2205,
"cds_end": null,
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{
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},
{
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"synonymous_variant"
],
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},
{
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"protein_coding": false,
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"non_coding_transcript_exon_variant"
],
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{
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{
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"non_coding_transcript_exon_variant"
],
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"feature": "NR_046554.1"
},
{
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"3_prime_UTR_variant"
],
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"biotype": "nonsense_mediated_decay",
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],
"gene_symbol": "CNTN4",
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"dbsnp": "rs112567538",
"frequency_reference_population": 0.0009905798,
"hom_count_reference_population": 20,
"allele_count_reference_population": 1599,
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"gnomad_exomes_ac": 832,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4000000059604645,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.838,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -18,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_175607.3",
"gene_symbol": "CNTN4",
"hgnc_id": 2174,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2205T>C",
"hgvs_p": "p.Tyr735Tyr"
},
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000442749.2",
"gene_symbol": "CNTN4-AS1",
"hgnc_id": 39985,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.595A>G",
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}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}