15-62099409-C-T

Variant names:

• chr15-62099409-C-T
• rs7163757

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 0.506 in 151,990 control chromosomes in the GnomAD database, including 20,530 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 0.51 (20530 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01
• Publications: 45 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.505 AC: 76767 AN: 151872 Hom.: 20470 Cov.: 33

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.506 AC: 76897 AN: 151990 Hom.: 20530 Cov.: 33 AF XY: 0.507 AC XY: 37683 AN XY: 74290

African (AFR) AF: 0.682 AC: 28292 AN: 41470

American (AMR) AF: 0.479 AC: 7307 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1180 AN: 3466

East Asian (EAS) AF: 0.364 AC: 1877 AN: 5162

South Asian (SAS) AF: 0.383 AC: 1846 AN: 4820

European-Finnish (FIN) AF: 0.557 AC: 5878 AN: 10548

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28882 AN: 67970

Other (OTH) AF: 0.494 AC: 1040 AN: 2106

Alfa AF: 0.450 Hom.: 45459

Bravo AF: 0.508

Asia WGS AF: 0.443 AC: 1537 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs7163757; hg19: chr15-62391608;