11-50502274-T-A

Variant names:

• chr11-50502274-T-A
• rs2204184

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 0.13 in 151,632 control chromosomes in the GnomAD database, including 1,499 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 0.13 (1499 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 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: 0.130 AC: 19752 AN: 151512 Hom.: 1496 Cov.: 33

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.130 AC: 19781 AN: 151632 Hom.: 1499 Cov.: 33 AF XY: 0.131 AC XY: 9737 AN XY: 74112

African (AFR) AF: 0.164 AC: 6815 AN: 41440

American (AMR) AF: 0.131 AC: 1988 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 371 AN: 3460

East Asian (EAS) AF: 0.242 AC: 1226 AN: 5056

South Asian (SAS) AF: 0.287 AC: 1384 AN: 4820

European-Finnish (FIN) AF: 0.0524 AC: 557 AN: 10622

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7078 AN: 67744

Other (OTH) AF: 0.125 AC: 263 AN: 2106

Alfa AF: 0.0459 Hom.: 41

Bravo AF: 0.135

Asia WGS AF: 0.281 AC: 975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.24

Splicing

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

Other links and lift over

dbSNP: rs2204184; hg19: chr11-50461445;