3-172454464-T-G

Variant names:

• chr3-172454464-T-G
• rs477441

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.817

Alfa AF: 0.816 Hom.: 6306

Bravo AF: 0.844

Asia WGS AF: 0.825 AC: 2866 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs477441; hg19: chr3-172172254;