3-12681371-A-G

Variant names:

• chr3-12681371-A-G
• rs6442323

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 0.493 in 151,944 control chromosomes in the GnomAD database, including 19,289 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 0.49 (19289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 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: 0.493 AC: 74870 AN: 151826 Hom.: 19288 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.493 AC: 74909 AN: 151944 Hom.: 19289 Cov.: 32 AF XY: 0.497 AC XY: 36925 AN XY: 74238

African (AFR) AF: 0.389 AC: 16129 AN: 41448

American (AMR) AF: 0.471 AC: 7180 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3470

East Asian (EAS) AF: 0.892 AC: 4614 AN: 5170

South Asian (SAS) AF: 0.748 AC: 3605 AN: 4818

European-Finnish (FIN) AF: 0.488 AC: 5138 AN: 10532

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34839 AN: 67946

Other (OTH) AF: 0.495 AC: 1046 AN: 2114

Alfa AF: 0.514 Hom.: 58932

Bravo AF: 0.481

Asia WGS AF: 0.722 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.7
DANN	Benign	0.64
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6442323; hg19: chr3-12722870;