3-166243323-A-G

Variant names:

• chr3-166243323-A-G
• rs1371901

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 0.688 in 151,852 control chromosomes in the GnomAD database, including 36,083 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 0.69 (36083 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.761 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: 0.688 AC: 104427 AN: 151732 Hom.: 36055 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.688 AC: 104517 AN: 151852 Hom.: 36083 Cov.: 31 AF XY: 0.696 AC XY: 51621 AN XY: 74196

African (AFR) AF: 0.669 AC: 27690 AN: 41418

American (AMR) AF: 0.665 AC: 10115 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2200 AN: 3472

East Asian (EAS) AF: 0.688 AC: 3526 AN: 5128

South Asian (SAS) AF: 0.782 AC: 3773 AN: 4824

European-Finnish (FIN) AF: 0.805 AC: 8507 AN: 10564

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.687 AC: 46669 AN: 67934

Other (OTH) AF: 0.665 AC: 1402 AN: 2108

Alfa AF: 0.684 Hom.: 114394

Bravo AF: 0.673

Asia WGS AF: 0.737 AC: 2562 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
DANN	Benign	0.61
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1371901; hg19: chr3-165961111;