rs894177

chr3-143175569-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;