11-3638062-A-G

Variant names:

• chr11-3638062-A-G
• rs11028690

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 0.262 in 152,082 control chromosomes in the GnomAD database, including 8,863 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 0.26 (8863 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39804 AN: 151960 Hom.: 8819 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.262 AC: 39905 AN: 152082 Hom.: 8863 Cov.: 32 AF XY: 0.256 AC XY: 19069 AN XY: 74350

African (AFR) AF: 0.613 AC: 25372 AN: 41420

American (AMR) AF: 0.189 AC: 2887 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3472

East Asian (EAS) AF: 0.158 AC: 816 AN: 5176

South Asian (SAS) AF: 0.0902 AC: 435 AN: 4820

European-Finnish (FIN) AF: 0.103 AC: 1094 AN: 10604

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8171 AN: 68002

Other (OTH) AF: 0.243 AC: 513 AN: 2110

Alfa AF: 0.177 Hom.: 1817

Bravo AF: 0.288

Asia WGS AF: 0.159 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.36
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs11028690; hg19: chr11-3659292;