11-50646073-G-C

Variant names:

• chr11-50646073-G-C
• rs2111306

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 0.584 in 150,190 control chromosomes in the GnomAD database, including 26,372 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 0.58 (26372 hom., cov: 31)
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.584 AC: 87648 AN: 150072 Hom.: 26346 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.584 AC: 87716 AN: 150190 Hom.: 26372 Cov.: 31 AF XY: 0.588 AC XY: 43067 AN XY: 73240

African (AFR) AF: 0.472 AC: 19453 AN: 41186

American (AMR) AF: 0.713 AC: 10709 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2447 AN: 3436

East Asian (EAS) AF: 0.778 AC: 3910 AN: 5026

South Asian (SAS) AF: 0.725 AC: 3486 AN: 4808

European-Finnish (FIN) AF: 0.563 AC: 5927 AN: 10528

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 39633 AN: 66898

Other (OTH) AF: 0.634 AC: 1315 AN: 2074

Alfa AF: 0.447 Hom.: 1213

Bravo AF: 0.591

Asia WGS AF: 0.746 AC: 2591 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.32

Splicing

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

Other links and lift over

dbSNP: rs2111306; hg19: chr11-50605244;