3-172454464-T-G

Variant names:

• chr3-172454464-T-G
• rs477441

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 0.834 in 152,202 control chromosomes in the GnomAD database, including 53,394 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 0.83 (53394 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.834 AC: 126867 AN: 152084 Hom.: 53325 Cov.: 33

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.834 AC: 126995 AN: 152202 Hom.: 53394 Cov.: 33 AF XY: 0.833 AC XY: 62005 AN XY: 74394

African (AFR) AF: 0.937 AC: 38919 AN: 41546

American (AMR) AF: 0.841 AC: 12857 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2490 AN: 3470

East Asian (EAS) AF: 0.763 AC: 3958 AN: 5186

South Asian (SAS) AF: 0.810 AC: 3903 AN: 4818

European-Finnish (FIN) AF: 0.817 AC: 8642 AN: 10580

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53601 AN: 67990

Other (OTH) AF: 0.817 AC: 1725 AN: 2112

Alfa AF: 0.821 Hom.: 6640

Bravo AF: 0.844

Asia WGS AF: 0.825 AC: 2866 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs477441; hg19: chr3-172172254;