rs634990

Positions:

• chr15-34713872-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.481 in 151,998 control chromosomes in the GnomAD database, including 17,728 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 0.48 (17728 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73024 AN: 151880 Hom.: 17713 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.481 AC: 73075 AN: 151998 Hom.: 17728 Cov.: 32 AF XY: 0.475 AC XY: 35278 AN XY: 74292

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.480

Alfa AF: 0.474 Hom.: 31010

Bravo AF: 0.486

Asia WGS AF: 0.532 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	15
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs634990; hg19: chr15-35006073;