rs17015762

Variant names:

• chr3-78007643-C-T
• rs17015762
• ENST00000756757.1:n.234+15158G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000756757.1(ENSG00000298601):​n.234+15158G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00493 in 152,204 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0049 (20 hom., cov: 32)
• Consequence: ENSG00000298601 ENST00000756757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 0 publications found

Genes affected

ENSG00000298601 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377171	XR_940977.4	n.215+15158G>A		intron_variant	Intron 2 of 6
LOC105377171	XR_940978.4	n.215+15158G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298601	ENST00000756757.1	n.234+15158G>A		intron_variant	Intron 2 of 5
ENSG00000298601	ENST00000756759.1	n.189+15158G>A		intron_variant	Intron 2 of 5
ENSG00000298601	ENST00000756760.1	n.220+15158G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.00496 AC: 754 AN: 152086 Hom.: 21 Cov.: 32

Gnomad AFR AF: 0.00106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0785

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000500

Gnomad OTH AF: 0.00479

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00493 AC: 750 AN: 152204 Hom.: 20 Cov.: 32 AF XY: 0.00568 AC XY: 423 AN XY: 74408

African (AFR) AF: 0.00106 AC: 44 AN: 41540

American (AMR) AF: 0.0134 AC: 205 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.0785 AC: 405 AN: 5160

South Asian (SAS) AF: 0.00373 AC: 18 AN: 4826

European-Finnish (FIN) AF: 0.00311 AC: 33 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000500 AC: 34 AN: 68010

Other (OTH) AF: 0.00474 AC: 10 AN: 2110

Alfa AF: 0.00453 Hom.: 53

Bravo AF: 0.00646

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.31
PhyloP100		0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17015762; hg19: chr3-78056794;