11-127560939-A-G

Variant names:

• chr11-127560939-A-G
• rs356248

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 0.769 in 152,114 control chromosomes in the GnomAD database, including 45,656 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 0.77 (45656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 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: 0.769 AC: 116894 AN: 151996 Hom.: 45601 Cov.: 32

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.769 AC: 117010 AN: 152114 Hom.: 45656 Cov.: 32 AF XY: 0.770 AC XY: 57268 AN XY: 74348

African (AFR) AF: 0.907 AC: 37689 AN: 41536

American (AMR) AF: 0.752 AC: 11489 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2635 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4471 AN: 5158

South Asian (SAS) AF: 0.688 AC: 3314 AN: 4814

European-Finnish (FIN) AF: 0.717 AC: 7577 AN: 10574

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47256 AN: 67956

Other (OTH) AF: 0.752 AC: 1590 AN: 2114

Alfa AF: 0.707 Hom.: 12485

Bravo AF: 0.781

Asia WGS AF: 0.745 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.032
DANN	Benign	0.40
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs356248; hg19: chr11-127430834;