15-96957080-G-T

Variant names:

• chr15-96957080-G-T
• rs9672547

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 0.492 in 151,998 control chromosomes in the GnomAD database, including 18,638 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 0.49 (18638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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: 0.492 AC: 74714 AN: 151880 Hom.: 18631 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.492 AC: 74755 AN: 151998 Hom.: 18638 Cov.: 32 AF XY: 0.487 AC XY: 36180 AN XY: 74288

African (AFR) AF: 0.567 AC: 23493 AN: 41462

American (AMR) AF: 0.417 AC: 6363 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3472

East Asian (EAS) AF: 0.409 AC: 2108 AN: 5158

South Asian (SAS) AF: 0.398 AC: 1915 AN: 4814

European-Finnish (FIN) AF: 0.431 AC: 4552 AN: 10554

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32924 AN: 67966

Other (OTH) AF: 0.491 AC: 1038 AN: 2114

Alfa AF: 0.484 Hom.: 56528

Bravo AF: 0.503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.21
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9672547; hg19: chr15-97500310;