11-4626540-T-G

Variant names:

• chr11-4626540-T-G
• rs3861787

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 0.849 in 151,926 control chromosomes in the GnomAD database, including 56,636 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 0.85 (56636 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.850 AC: 128963 AN: 151810 Hom.: 56624 Cov.: 30

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.849 AC: 129010 AN: 151926 Hom.: 56636 Cov.: 30 AF XY: 0.856 AC XY: 63548 AN XY: 74266

African (AFR) AF: 0.600 AC: 24817 AN: 41330

American (AMR) AF: 0.909 AC: 13878 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3334 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5118 AN: 5122

South Asian (SAS) AF: 0.979 AC: 4722 AN: 4822

European-Finnish (FIN) AF: 0.983 AC: 10415 AN: 10590

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63710 AN: 68002

Other (OTH) AF: 0.866 AC: 1828 AN: 2112

Alfa AF: 0.906 Hom.: 190326

Bravo AF: 0.834

Asia WGS AF: 0.961 AC: 3342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.6
DANN	Benign	0.31
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs3861787; hg19: chr11-4647770;