rs2139424

Positions:

• chr11-20662494-G-C

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 0.182 in 152,224 control chromosomes in the GnomAD database, including 2,717 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 0.18 (2717 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27694 AN: 152106 Hom.: 2718 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.182 AC: 27703 AN: 152224 Hom.: 2717 Cov.: 33 AF XY: 0.179 AC XY: 13352 AN XY: 74414

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0666

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.170

Alfa AF: 0.199 Hom.: 393

Bravo AF: 0.173

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2139424; hg19: chr11-20684040;