chr11-50405890-A-G

Position:

• chr11-50405890-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.695

Alfa AF: 0.646 Hom.: 3816

Bravo AF: 0.654

Asia WGS AF: 0.769 AC: 2672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs692427; hg19: chr11-50365061;