11-67596446-A-G

Variant names:

• chr11-67596446-A-G
• rs2169650

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 0.94 in 152,256 control chromosomes in the GnomAD database, including 67,289 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 0.94 (67289 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.941 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: 0.940 AC: 143038 AN: 152138 Hom.: 67238 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.940

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.940 AC: 143147 AN: 152256 Hom.: 67289 Cov.: 31 AF XY: 0.940 AC XY: 69972 AN XY: 74456

African (AFR) AF: 0.937 AC: 38909 AN: 41546

American (AMR) AF: 0.950 AC: 14522 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3212 AN: 3472

East Asian (EAS) AF: 0.863 AC: 4462 AN: 5168

South Asian (SAS) AF: 0.938 AC: 4531 AN: 4832

European-Finnish (FIN) AF: 0.940 AC: 9984 AN: 10618

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64400 AN: 68018

Other (OTH) AF: 0.937 AC: 1975 AN: 2108

Alfa AF: 0.940 Hom.: 36104

Bravo AF: 0.940

Asia WGS AF: 0.910 AC: 3165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.93
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2169650; hg19: chr11-67363917;