11-62432345-T-C

Variant names:

• chr11-62432345-T-C
• rs17157266

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 0.147 in 152,076 control chromosomes in the GnomAD database, including 2,031 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 0.15 (2031 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 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: 0.147 AC: 22323 AN: 151958 Hom.: 2025 Cov.: 30

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.147 AC: 22339 AN: 152076 Hom.: 2031 Cov.: 30 AF XY: 0.150 AC XY: 11169 AN XY: 74336

African (AFR) AF: 0.0449 AC: 1863 AN: 41524

American (AMR) AF: 0.191 AC: 2914 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3468

East Asian (EAS) AF: 0.264 AC: 1362 AN: 5164

South Asian (SAS) AF: 0.346 AC: 1664 AN: 4816

European-Finnish (FIN) AF: 0.144 AC: 1517 AN: 10568

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11828 AN: 67964

Other (OTH) AF: 0.157 AC: 331 AN: 2108

Alfa AF: 0.166 Hom.: 4886

Bravo AF: 0.142

Asia WGS AF: 0.279 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs17157266; hg19: chr11-62199817;