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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: 4-87982853-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=87982853&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 87982853,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000395080.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.902G>C",
"hgvs_p": "p.Arg301Pro",
"transcript": "NM_001040058.2",
"protein_id": "NP_001035147.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 314,
"cds_start": 902,
"cds_end": null,
"cds_length": 945,
"cdna_start": 1003,
"cdna_end": null,
"cdna_length": 1561,
"mane_select": "ENST00000395080.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.902G>C",
"hgvs_p": "p.Arg301Pro",
"transcript": "ENST00000395080.8",
"protein_id": "ENSP00000378517.3",
"transcript_support_level": 1,
"aa_start": 301,
"aa_end": null,
"aa_length": 314,
"cds_start": 902,
"cds_end": null,
"cds_length": 945,
"cdna_start": 1003,
"cdna_end": null,
"cdna_length": 1561,
"mane_select": "NM_001040058.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.860G>C",
"hgvs_p": "p.Arg287Pro",
"transcript": "ENST00000237623.11",
"protein_id": "ENSP00000237623.7",
"transcript_support_level": 1,
"aa_start": 287,
"aa_end": null,
"aa_length": 300,
"cds_start": 860,
"cds_end": null,
"cds_length": 903,
"cdna_start": 1008,
"cdna_end": null,
"cdna_length": 1581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.821G>C",
"hgvs_p": "p.Arg274Pro",
"transcript": "ENST00000360804.4",
"protein_id": "ENSP00000354042.4",
"transcript_support_level": 1,
"aa_start": 274,
"aa_end": null,
"aa_length": 287,
"cds_start": 821,
"cds_end": null,
"cds_length": 864,
"cdna_start": 922,
"cdna_end": null,
"cdna_length": 1196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1191G>C",
"hgvs_p": null,
"transcript": "ENST00000509659.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.941G>C",
"hgvs_p": "p.Arg314Pro",
"transcript": "NM_001251830.2",
"protein_id": "NP_001238759.1",
"transcript_support_level": null,
"aa_start": 314,
"aa_end": null,
"aa_length": 327,
"cds_start": 941,
"cds_end": null,
"cds_length": 984,
"cdna_start": 1192,
"cdna_end": null,
"cdna_length": 1750,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.902G>C",
"hgvs_p": "p.Arg301Pro",
"transcript": "ENST00000614857.5",
"protein_id": "ENSP00000477824.2",
"transcript_support_level": 2,
"aa_start": 301,
"aa_end": null,
"aa_length": 314,
"cds_start": 902,
"cds_end": null,
"cds_length": 945,
"cdna_start": 1052,
"cdna_end": null,
"cdna_length": 1728,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.860G>C",
"hgvs_p": "p.Arg287Pro",
"transcript": "NM_000582.3",
"protein_id": "NP_000573.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 300,
"cds_start": 860,
"cds_end": null,
"cds_length": 903,
"cdna_start": 961,
"cdna_end": null,
"cdna_length": 1519,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.821G>C",
"hgvs_p": "p.Arg274Pro",
"transcript": "NM_001040060.2",
"protein_id": "NP_001035149.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 287,
"cds_start": 821,
"cds_end": null,
"cds_length": 864,
"cdna_start": 922,
"cdna_end": null,
"cdna_length": 1480,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.779G>C",
"hgvs_p": "p.Arg260Pro",
"transcript": "NM_001251829.2",
"protein_id": "NP_001238758.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 273,
"cds_start": 779,
"cds_end": null,
"cds_length": 822,
"cdna_start": 880,
"cdna_end": null,
"cdna_length": 1438,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.779G>C",
"hgvs_p": "p.Arg260Pro",
"transcript": "ENST00000508233.6",
"protein_id": "ENSP00000422973.2",
"transcript_support_level": 2,
"aa_start": 260,
"aa_end": null,
"aa_length": 273,
"cds_start": 779,
"cds_end": null,
"cds_length": 822,
"cdna_start": 880,
"cdna_end": null,
"cdna_length": 923,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1129G>C",
"hgvs_p": null,
"transcript": "ENST00000681973.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1808,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.855G>C",
"hgvs_p": null,
"transcript": "ENST00000682026.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.2388G>C",
"hgvs_p": null,
"transcript": "ENST00000682448.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 3064,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.2350G>C",
"hgvs_p": null,
"transcript": "ENST00000682554.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.3390G>C",
"hgvs_p": null,
"transcript": "ENST00000682599.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 4066,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.822G>C",
"hgvs_p": null,
"transcript": "ENST00000682627.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 1498,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1186G>C",
"hgvs_p": null,
"transcript": "ENST00000682865.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1862,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.916G>C",
"hgvs_p": null,
"transcript": "ENST00000683087.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1656G>C",
"hgvs_p": null,
"transcript": "ENST00000683168.1",
"protein_id": null,
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"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.2084G>C",
"hgvs_p": null,
"transcript": "ENST00000683620.1",
"protein_id": null,
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"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 2760,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.3152G>C",
"hgvs_p": null,
"transcript": "ENST00000684106.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1961G>C",
"hgvs_p": null,
"transcript": "ENST00000684450.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 2637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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{
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"intron_variant"
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}
],
"gene_symbol": "SPP1",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
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"gnomad_exomes_homalt": 0,
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"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5606248378753662,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.178,
"revel_prediction": "Benign",
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"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.415,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000395080.8",
"gene_symbol": "SPP1",
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"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.902G>C",
"hgvs_p": "p.Arg301Pro"
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{
"score": 2,
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"pathogenic_score": 2,
"criteria": [
"PM2"
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"verdict": "Uncertain_significance",
"transcript": "ENST00000662475.1",
"gene_symbol": "ENSG00000286618",
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"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.307+6505C>G",
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}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}