chr11-50405890-A-G

Variant names:

• chr11-50405890-A-G
• rs692427

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 0.648 in 151,350 control chromosomes in the GnomAD database, including 32,365 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 0.65 (32365 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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: 0.648 AC: 98067 AN: 151230 Hom.: 32339 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.648 AC: 98137 AN: 151350 Hom.: 32365 Cov.: 31 AF XY: 0.651 AC XY: 48128 AN XY: 73910

African (AFR) AF: 0.562 AC: 23234 AN: 41338

American (AMR) AF: 0.757 AC: 11459 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2555 AN: 3458

East Asian (EAS) AF: 0.776 AC: 3961 AN: 5104

South Asian (SAS) AF: 0.768 AC: 3701 AN: 4816

European-Finnish (FIN) AF: 0.621 AC: 6555 AN: 10552

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.656 AC: 44360 AN: 67638

Other (OTH) AF: 0.695 AC: 1463 AN: 2104

Alfa AF: 0.643 Hom.: 3938

Bravo AF: 0.654

Asia WGS AF: 0.769 AC: 2672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.35
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs692427; hg19: chr11-50365061;