3-172459150-A-G

Variant names:

• chr3-172459150-A-G
• rs474225

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 0.817 in 152,174 control chromosomes in the GnomAD database, including 50,991 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 (50991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 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: 0.817 AC: 124199 AN: 152056 Hom.: 50924 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.817 AC: 124325 AN: 152174 Hom.: 50991 Cov.: 32 AF XY: 0.817 AC XY: 60741 AN XY: 74382

African (AFR) AF: 0.880 AC: 36545 AN: 41524

American (AMR) AF: 0.834 AC: 12742 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2490 AN: 3472

East Asian (EAS) AF: 0.765 AC: 3954 AN: 5170

South Asian (SAS) AF: 0.809 AC: 3901 AN: 4824

European-Finnish (FIN) AF: 0.816 AC: 8644 AN: 10590

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53459 AN: 68008

Other (OTH) AF: 0.802 AC: 1693 AN: 2110

Alfa AF: 0.799 Hom.: 73409

Bravo AF: 0.824

Asia WGS AF: 0.822 AC: 2856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.39
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs474225; hg19: chr3-172176940;