rs894177

Variant names:

• chr3-143175569-G-A
• rs894177

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 0.741 in 152,200 control chromosomes in the GnomAD database, including 42,922 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 0.74 (42922 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 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: 0.741 AC: 112661 AN: 152082 Hom.: 42850 Cov.: 33

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.741 AC: 112789 AN: 152200 Hom.: 42922 Cov.: 33 AF XY: 0.736 AC XY: 54794 AN XY: 74406

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.722

Alfa AF: 0.674 Hom.: 25936

Bravo AF: 0.763

Asia WGS AF: 0.677 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs894177; hg19: chr3-142894411;