11-76255567-A-G

Variant names:

• chr11-76255567-A-G
• rs2510733

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 0.589 in 152,026 control chromosomes in the GnomAD database, including 26,700 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 0.59 (26700 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 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: 0.589 AC: 89453 AN: 151908 Hom.: 26672 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.589 AC: 89533 AN: 152026 Hom.: 26700 Cov.: 32 AF XY: 0.591 AC XY: 43909 AN XY: 74300

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.575

Alfa AF: 0.538 Hom.: 27561

Bravo AF: 0.590

Asia WGS AF: 0.676 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2510733; hg19: chr11-75966611;