rs2139424

Variant names:

• chr11-20662494-G-C
• rs2139424

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 0.182 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.172 AC: 7127 AN: 41540

American (AMR) AF: 0.121 AC: 1850 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3472

East Asian (EAS) AF: 0.0666 AC: 345 AN: 5180

South Asian (SAS) AF: 0.187 AC: 904 AN: 4822

European-Finnish (FIN) AF: 0.185 AC: 1961 AN: 10584

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.214 AC: 14566 AN: 68006

Other (OTH) AF: 0.170 AC: 360 AN: 2114

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2139424; hg19: chr11-20684040;