rs961235

chr15-70157755-C-T

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 0.0969 in 152,122 control chromosomes in the GnomAD database, including 824 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 0.097 (824 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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: 0.0967 AC: 14700 AN: 152004 Hom.: 819 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0812

Gnomad OTH AF: 0.0954

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

GnomAD4 genome AF: 0.0969 AC: 14740 AN: 152122 Hom.: 824 Cov.: 32 AF XY: 0.0947 AC XY: 7041 AN XY: 74382

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.0342

Gnomad4 SAS AF: 0.0576

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.0812

Gnomad4 OTH AF: 0.0939

Alfa AF: 0.0924 Hom.: 179

Bravo AF: 0.105

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.9
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs961235; hg19: chr15-70450094;