chr3-172441134-A-G

Variant names:

• chr3-172441134-A-G
• rs1916345

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 0.776 in 152,138 control chromosomes in the GnomAD database, including 46,737 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 0.78 (46737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117970 AN: 152020 Hom.: 46716 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.776 AC: 118033 AN: 152138 Hom.: 46737 Cov.: 32 AF XY: 0.782 AC XY: 58140 AN XY: 74390

African (AFR) AF: 0.613 AC: 25436 AN: 41464

American (AMR) AF: 0.836 AC: 12778 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2544 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5161 AN: 5190

South Asian (SAS) AF: 0.808 AC: 3892 AN: 4816

European-Finnish (FIN) AF: 0.914 AC: 9686 AN: 10598

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55824 AN: 68004

Other (OTH) AF: 0.783 AC: 1648 AN: 2106

Alfa AF: 0.793 Hom.: 16577

Bravo AF: 0.764

Asia WGS AF: 0.887 AC: 3087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.34
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs1916345; hg19: chr3-172158924;