15-85155976-G-C

Variant names:

• chr15-85155976-G-C
• rs8040855

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 0.645 in 152,080 control chromosomes in the GnomAD database, including 32,150 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 (32150 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97953 AN: 151962 Hom.: 32115 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.645 AC: 98052 AN: 152080 Hom.: 32150 Cov.: 32 AF XY: 0.652 AC XY: 48437 AN XY: 74342

African (AFR) AF: 0.611 AC: 25342 AN: 41466

American (AMR) AF: 0.712 AC: 10890 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1963 AN: 3464

East Asian (EAS) AF: 0.969 AC: 5013 AN: 5174

South Asian (SAS) AF: 0.811 AC: 3910 AN: 4824

European-Finnish (FIN) AF: 0.660 AC: 6971 AN: 10564

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42085 AN: 67976

Other (OTH) AF: 0.622 AC: 1313 AN: 2112

Alfa AF: 0.526 Hom.: 1591

Bravo AF: 0.643

Asia WGS AF: 0.874 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.43
DANN	Benign	0.72
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs8040855; hg19: chr15-85699207;