3-46304120-G-A

Variant names:

• chr3-46304120-G-A
• rs11711054

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 0.726 in 152,100 control chromosomes in the GnomAD database, including 40,354 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 0.73 (40354 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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: 0.726 AC: 110313 AN: 151982 Hom.: 40298 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.726 AC: 110419 AN: 152100 Hom.: 40354 Cov.: 32 AF XY: 0.722 AC XY: 53708 AN XY: 74340

African (AFR) AF: 0.817 AC: 33889 AN: 41502

American (AMR) AF: 0.670 AC: 10231 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2549 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3603 AN: 5174

South Asian (SAS) AF: 0.657 AC: 3164 AN: 4816

European-Finnish (FIN) AF: 0.713 AC: 7526 AN: 10560

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.694 AC: 47168 AN: 67986

Other (OTH) AF: 0.709 AC: 1498 AN: 2114

Alfa AF: 0.705 Hom.: 23633

Bravo AF: 0.731

Asia WGS AF: 0.706 AC: 2453 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.47
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs11711054; hg19: chr3-46345611;