3-12443350-A-G

Variant names:

• chr3-12443350-A-G
• rs4684104

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 0.468 in 152,010 control chromosomes in the GnomAD database, including 20,443 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 0.47 (20443 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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: 0.469 AC: 71203 AN: 151892 Hom.: 20448 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.468 AC: 71201 AN: 152010 Hom.: 20443 Cov.: 31 AF XY: 0.478 AC XY: 35511 AN XY: 74308

African (AFR) AF: 0.143 AC: 5924 AN: 41482

American (AMR) AF: 0.462 AC: 7050 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1749 AN: 3468

East Asian (EAS) AF: 0.930 AC: 4791 AN: 5152

South Asian (SAS) AF: 0.715 AC: 3453 AN: 4826

European-Finnish (FIN) AF: 0.687 AC: 7250 AN: 10558

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39389 AN: 67958

Other (OTH) AF: 0.455 AC: 954 AN: 2098

Alfa AF: 0.540 Hom.: 43588

Bravo AF: 0.436

Asia WGS AF: 0.686 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.55
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs4684104; hg19: chr3-12484849;