rs7173964

Variant names:

• chr15-62104743-G-A
• rs7173964

Variant summary

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

The variant allele was found at a frequency of 0.484 in 152,182 control chromosomes in the GnomAD database, including 18,389 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 0.48 (18389 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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: 0.484 AC: 73548 AN: 152064 Hom.: 18341 Cov.: 34

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.484 AC: 73664 AN: 152182 Hom.: 18389 Cov.: 34 AF XY: 0.486 AC XY: 36166 AN XY: 74392

African (AFR) AF: 0.609 AC: 25293 AN: 41510

American (AMR) AF: 0.467 AC: 7152 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1179 AN: 3470

East Asian (EAS) AF: 0.371 AC: 1920 AN: 5182

South Asian (SAS) AF: 0.383 AC: 1849 AN: 4822

European-Finnish (FIN) AF: 0.555 AC: 5873 AN: 10580

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28791 AN: 67996

Other (OTH) AF: 0.479 AC: 1014 AN: 2116

Alfa AF: 0.439 Hom.: 44250

Bravo AF: 0.482

Asia WGS AF: 0.440 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.026
DANN	Benign	0.57
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7173964; hg19: chr15-62396942;