11-127596868-A-G

Variant names:

• chr11-127596868-A-G
• rs763300

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 0.619 in 152,100 control chromosomes in the GnomAD database, including 29,516 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 0.62 (29516 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• 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 (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.619 AC: 94096 AN: 151982 Hom.: 29496 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.619 AC: 94175 AN: 152100 Hom.: 29516 Cov.: 32 AF XY: 0.626 AC XY: 46505 AN XY: 74336

African (AFR) AF: 0.668 AC: 27691 AN: 41482

American (AMR) AF: 0.594 AC: 9080 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2260 AN: 3468

East Asian (EAS) AF: 0.836 AC: 4318 AN: 5166

South Asian (SAS) AF: 0.569 AC: 2747 AN: 4832

European-Finnish (FIN) AF: 0.681 AC: 7199 AN: 10570

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38756 AN: 67982

Other (OTH) AF: 0.605 AC: 1277 AN: 2110

Alfa AF: 0.580 Hom.: 12968

Bravo AF: 0.621

Asia WGS AF: 0.648 AC: 2251 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	0.89
DANN	Benign	0.41
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs763300; hg19: chr11-127466763;