11-56842936-G-T

Variant names:

• chr11-56842936-G-T
• rs764855

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 0.507 in 151,624 control chromosomes in the GnomAD database, including 20,027 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 0.51 (20027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.863
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76750 AN: 151506 Hom.: 19993 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.507 AC: 76840 AN: 151624 Hom.: 20027 Cov.: 32 AF XY: 0.516 AC XY: 38214 AN XY: 74112

African (AFR) AF: 0.582 AC: 24032 AN: 41288

American (AMR) AF: 0.536 AC: 8171 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3462

East Asian (EAS) AF: 0.686 AC: 3517 AN: 5126

South Asian (SAS) AF: 0.662 AC: 3181 AN: 4808

European-Finnish (FIN) AF: 0.548 AC: 5768 AN: 10528

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29184 AN: 67868

Other (OTH) AF: 0.501 AC: 1053 AN: 2102

Alfa AF: 0.455 Hom.: 63650

Bravo AF: 0.507

Asia WGS AF: 0.691 AC: 2404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs764855; hg19: chr11-56610412;