15-48391257-T-G

Variant names:

• chr15-48391257-T-G
• rs8031017

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 0.665 in 152,146 control chromosomes in the GnomAD database, including 36,617 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 0.67 (36617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.808 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: 0.666 AC: 101200 AN: 152028 Hom.: 36629 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.665 AC: 101215 AN: 152146 Hom.: 36617 Cov.: 32 AF XY: 0.667 AC XY: 49638 AN XY: 74368

African (AFR) AF: 0.365 AC: 15144 AN: 41494

American (AMR) AF: 0.740 AC: 11314 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2784 AN: 3470

East Asian (EAS) AF: 0.496 AC: 2565 AN: 5172

South Asian (SAS) AF: 0.680 AC: 3274 AN: 4812

European-Finnish (FIN) AF: 0.785 AC: 8316 AN: 10588

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55316 AN: 68008

Other (OTH) AF: 0.691 AC: 1461 AN: 2114

Alfa AF: 0.757 Hom.: 8469

Bravo AF: 0.650

Asia WGS AF: 0.545 AC: 1899 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.59
DANN	Benign	0.63
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs8031017; hg19: chr15-48683454;