15-78325571-T-C

Variant names:

• chr15-78325571-T-C
• rs8027394

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 0.701 in 152,098 control chromosomes in the GnomAD database, including 37,719 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 0.70 (37719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 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: 0.701 AC: 106572 AN: 151980 Hom.: 37681 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.701 AC: 106663 AN: 152098 Hom.: 37719 Cov.: 32 AF XY: 0.699 AC XY: 51984 AN XY: 74372

African (AFR) AF: 0.794 AC: 32941 AN: 41464

American (AMR) AF: 0.663 AC: 10140 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2073 AN: 3468

East Asian (EAS) AF: 0.535 AC: 2765 AN: 5170

South Asian (SAS) AF: 0.612 AC: 2956 AN: 4828

European-Finnish (FIN) AF: 0.659 AC: 6969 AN: 10578

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.687 AC: 46735 AN: 67986

Other (OTH) AF: 0.660 AC: 1393 AN: 2112

Alfa AF: 0.683 Hom.: 19473

Bravo AF: 0.705

Asia WGS AF: 0.551 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.31
DANN	Benign	0.55
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs8027394; hg19: chr15-78617913;