11-76255567-A-G

Variant names:

• chr11-76255567-A-G
• rs2510733

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 0.589 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.651 AC: 26974 AN: 41462

American (AMR) AF: 0.585 AC: 8936 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2027 AN: 3468

East Asian (EAS) AF: 0.686 AC: 3535 AN: 5152

South Asian (SAS) AF: 0.699 AC: 3375 AN: 4828

European-Finnish (FIN) AF: 0.574 AC: 6061 AN: 10556

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.540 AC: 36678 AN: 67962

Other (OTH) AF: 0.575 AC: 1212 AN: 2108

Alfa AF: 0.545 Hom.: 36427

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2510733; hg19: chr11-75966611;