15-91668544-G-A

Variant names:

• chr15-91668544-G-A
• rs7164176

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 0.643 in 152,104 control chromosomes in the GnomAD database, including 32,985 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 0.64 (32985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.828
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97712 AN: 151986 Hom.: 32930 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.643 AC: 97824 AN: 152104 Hom.: 32985 Cov.: 32 AF XY: 0.646 AC XY: 48005 AN XY: 74358

African (AFR) AF: 0.849 AC: 35262 AN: 41518

American (AMR) AF: 0.643 AC: 9827 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1537 AN: 3470

East Asian (EAS) AF: 0.803 AC: 4152 AN: 5168

South Asian (SAS) AF: 0.590 AC: 2848 AN: 4824

European-Finnish (FIN) AF: 0.581 AC: 6139 AN: 10566

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36190 AN: 67968

Other (OTH) AF: 0.605 AC: 1276 AN: 2108

Alfa AF: 0.569 Hom.: 82588

Bravo AF: 0.656

Asia WGS AF: 0.689 AC: 2392 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.39
DANN	Benign	0.38
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs7164176; hg19: chr15-92211774;