chr11-40049473-G-A

Variant names:

• chr11-40049473-G-A
• rs10837325

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.787 in 152,002 control chromosomes in the GnomAD database, including 47,566 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 0.79 (47566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 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: 0.787 AC: 119460 AN: 151884 Hom.: 47523 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.787 AC: 119569 AN: 152002 Hom.: 47566 Cov.: 32 AF XY: 0.783 AC XY: 58159 AN XY: 74272

African (AFR) AF: 0.686 AC: 28420 AN: 41456

American (AMR) AF: 0.797 AC: 12161 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2984 AN: 3468

East Asian (EAS) AF: 0.593 AC: 3029 AN: 5112

South Asian (SAS) AF: 0.829 AC: 3995 AN: 4820

European-Finnish (FIN) AF: 0.779 AC: 8248 AN: 10590

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58016 AN: 67984

Other (OTH) AF: 0.797 AC: 1680 AN: 2108

Alfa AF: 0.838 Hom.: 29102

Bravo AF: 0.783

Asia WGS AF: 0.729 AC: 2535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	13
DANN	Benign	0.63
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10837325; hg19: chr11-40071023;