15-92341827-C-T

Variant names:

• chr15-92341827-C-T
• rs11634097

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 0.113 in 152,178 control chromosomes in the GnomAD database, including 1,037 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 0.11 (1037 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.113 AC: 17152 AN: 152060 Hom.: 1039 Cov.: 32

Gnomad AFR AF: 0.0965

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.0841

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.113 AC: 17144 AN: 152178 Hom.: 1037 Cov.: 32 AF XY: 0.108 AC XY: 8059 AN XY: 74398

African (AFR) AF: 0.0962 AC: 3992 AN: 41516

American (AMR) AF: 0.0839 AC: 1283 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3470

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.0623 AC: 301 AN: 4828

European-Finnish (FIN) AF: 0.119 AC: 1254 AN: 10580

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9468 AN: 67994

Other (OTH) AF: 0.116 AC: 244 AN: 2108

Alfa AF: 0.101 Hom.: 549

Bravo AF: 0.111

Asia WGS AF: 0.0280 AC: 96 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs11634097; hg19: chr15-92885057; COSMIC: COSV56529529;