11-56474785-G-T

Variant names:

• chr11-56474785-G-T
• rs7939886

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 0.111 in 152,072 control chromosomes in the GnomAD database, including 1,067 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 0.11 (1067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16944 AN: 151954 Hom.: 1069 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0909

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

GnomAD4 genome AF: 0.111 AC: 16934 AN: 152072 Hom.: 1067 Cov.: 32 AF XY: 0.115 AC XY: 8511 AN XY: 74296

African (AFR) AF: 0.0803 AC: 3330 AN: 41492

American (AMR) AF: 0.0952 AC: 1454 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3470

East Asian (EAS) AF: 0.143 AC: 737 AN: 5170

South Asian (SAS) AF: 0.119 AC: 573 AN: 4816

European-Finnish (FIN) AF: 0.198 AC: 2087 AN: 10548

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8134 AN: 67988

Other (OTH) AF: 0.0890 AC: 188 AN: 2112

Alfa AF: 0.111 Hom.: 1799

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.43
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs7939886; hg19: chr11-56242261;