rs7164176

chr15-91668544-G-Achr15-91668544-G-Cchr15-91668544-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.803

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.605

Alfa AF: 0.539 Hom.: 26596

Bravo AF: 0.656

Asia WGS AF: 0.689 AC: 2392 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.39
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7164176; hg19: chr15-92211774;