rs7496513

Variant names:

• chr15-72998351-G-A
• rs7496513

Your query was ambiguous. Multiple possible variants found:

• chr15-72998351-G-A
• chr15-72998351-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.806 in 152,062 control chromosomes in the GnomAD database, including 50,169 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 0.81 (50169 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122461 AN: 151944 Hom.: 50117 Cov.: 30

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.806 AC: 122569 AN: 152062 Hom.: 50169 Cov.: 30 AF XY: 0.802 AC XY: 59653 AN XY: 74334

African (AFR) AF: 0.942 AC: 39088 AN: 41508

American (AMR) AF: 0.698 AC: 10663 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2683 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2805 AN: 5140

South Asian (SAS) AF: 0.717 AC: 3445 AN: 4808

European-Finnish (FIN) AF: 0.831 AC: 8787 AN: 10574

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52526 AN: 67974

Other (OTH) AF: 0.803 AC: 1696 AN: 2112

Alfa AF: 0.786 Hom.: 24745

Bravo AF: 0.804

Asia WGS AF: 0.645 AC: 2246 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	14
DANN	Benign	0.90
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs7496513; hg19: chr15-73290692;