15-78325571-T-C

Variant names:

• chr15-78325571-T-C
• rs8027394

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 0.701 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.701 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

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.660

Alfa AF: 0.682 Hom.: 17427

Bravo AF: 0.705

Asia WGS AF: 0.551 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8027394; hg19: chr15-78617913;