15-48077906-G-T

Variant names:

• chr15-48077906-G-T
• rs16960541

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 0.0836 in 152,184 control chromosomes in the GnomAD database, including 689 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 0.084 (689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.138 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: 0.0834 AC: 12682 AN: 152068 Hom.: 682 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0466

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.0836 AC: 12718 AN: 152184 Hom.: 689 Cov.: 32 AF XY: 0.0840 AC XY: 6246 AN XY: 74398

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0930

Gnomad4 FIN AF: 0.0298

Gnomad4 NFE AF: 0.0466

Gnomad4 OTH AF: 0.0960

Alfa AF: 0.0640 Hom.: 118

Bravo AF: 0.0943

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	2.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960541; hg19: chr15-48370103;