4-147712277-A-G

Variant names:

• chr4-147712277-A-G
• rs11099666

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 0.819 in 151,998 control chromosomes in the GnomAD database, including 52,450 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 0.82 (52450 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124500 AN: 151880 Hom.: 52437 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.819 AC: 124547 AN: 151998 Hom.: 52450 Cov.: 31 AF XY: 0.823 AC XY: 61133 AN XY: 74280

African (AFR) AF: 0.610 AC: 25249 AN: 41398

American (AMR) AF: 0.901 AC: 13768 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3096 AN: 3472

East Asian (EAS) AF: 0.733 AC: 3785 AN: 5166

South Asian (SAS) AF: 0.826 AC: 3974 AN: 4814

European-Finnish (FIN) AF: 0.971 AC: 10257 AN: 10566

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61683 AN: 67990

Other (OTH) AF: 0.827 AC: 1744 AN: 2110

Alfa AF: 0.889 Hom.: 41740

Bravo AF: 0.805

Asia WGS AF: 0.799 AC: 2778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.64
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs11099666; hg19: chr4-148633428;