chr11-76639075-G-C

Variant names:

• chr11-76639075-G-C
• rs12277366

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 0.609 in 152,014 control chromosomes in the GnomAD database, including 29,652 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 0.61 (29652 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 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: 0.609 AC: 92510 AN: 151896 Hom.: 29603 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.609 AC: 92614 AN: 152014 Hom.: 29652 Cov.: 31 AF XY: 0.608 AC XY: 45129 AN XY: 74286

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.579

Alfa AF: 0.575 Hom.: 2678

Bravo AF: 0.610

Asia WGS AF: 0.635 AC: 2212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12277366; hg19: chr11-76350119;