11-127560939-A-G

Variant names:

• chr11-127560939-A-G
• rs356248

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 0.769 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.752

Alfa AF: 0.701 Hom.: 7069

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs356248; hg19: chr11-127430834;