11-50646073-G-C

Variant names:

• chr11-50646073-G-C
• rs2111306

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 0.584 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.634

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 v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs2111306; hg19: chr11-50605244;