11-4655747-G-T

Variant names:

• chr11-4655747-G-T
• rs7926081

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 0.419 in 151,860 control chromosomes in the GnomAD database, including 14,180 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 0.42 (14180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 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: 0.419 AC: 63533 AN: 151740 Hom.: 14173 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.419 AC: 63569 AN: 151860 Hom.: 14180 Cov.: 31 AF XY: 0.411 AC XY: 30514 AN XY: 74202

African (AFR) AF: 0.323 AC: 13381 AN: 41404

American (AMR) AF: 0.442 AC: 6748 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1663 AN: 3468

East Asian (EAS) AF: 0.0413 AC: 213 AN: 5152

South Asian (SAS) AF: 0.369 AC: 1770 AN: 4802

European-Finnish (FIN) AF: 0.391 AC: 4120 AN: 10536

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34333 AN: 67926

Other (OTH) AF: 0.428 AC: 900 AN: 2102

Alfa AF: 0.452 Hom.: 7725

Bravo AF: 0.413

Asia WGS AF: 0.214 AC: 749 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.65
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs7926081; hg19: chr11-4676977;