15-70157755-C-T

Variant names:

• chr15-70157755-C-T
• rs961235

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;