11-21647747-G-A

Variant names:

• chr11-21647747-G-A
• rs10833583

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 0.0969 in 152,104 control chromosomes in the GnomAD database, including 893 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 0.097 (893 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0970 AC: 14738 AN: 151988 Hom.: 893 Cov.: 31

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0969 AC: 14734 AN: 152104 Hom.: 893 Cov.: 31 AF XY: 0.0981 AC XY: 7294 AN XY: 74318

African (AFR) AF: 0.0284 AC: 1178 AN: 41526

American (AMR) AF: 0.0769 AC: 1175 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3472

East Asian (EAS) AF: 0.122 AC: 628 AN: 5150

South Asian (SAS) AF: 0.112 AC: 537 AN: 4812

European-Finnish (FIN) AF: 0.158 AC: 1670 AN: 10568

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8704 AN: 67982

Other (OTH) AF: 0.100 AC: 211 AN: 2110

Alfa AF: 0.108 Hom.: 1552

Bravo AF: 0.0876

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10833583; hg19: chr11-21669293;