15-79777420-T-C

Variant names:

• chr15-79777420-T-C
• rs166870

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 0.696 in 152,122 control chromosomes in the GnomAD database, including 37,087 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 (37087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 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: 0.696 AC: 105845 AN: 152004 Hom.: 37045 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.696 AC: 105937 AN: 152122 Hom.: 37087 Cov.: 32 AF XY: 0.699 AC XY: 51945 AN XY: 74354

African (AFR) AF: 0.666 AC: 27606 AN: 41480

American (AMR) AF: 0.676 AC: 10344 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2504 AN: 3466

East Asian (EAS) AF: 0.855 AC: 4419 AN: 5168

South Asian (SAS) AF: 0.759 AC: 3656 AN: 4818

European-Finnish (FIN) AF: 0.713 AC: 7549 AN: 10588

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.700 AC: 47596 AN: 67994

Other (OTH) AF: 0.714 AC: 1510 AN: 2114

Alfa AF: 0.733 Hom.: 9872

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.80
DANN	Benign	0.76
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs166870; hg19: chr15-80069762;