chr3-134473096-C-T

Variant names:

• chr3-134473096-C-T
• rs9841212

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 0.623 in 152,088 control chromosomes in the GnomAD database, including 30,340 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 0.62 (30340 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 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: 0.624 AC: 94807 AN: 151970 Hom.: 30351 Cov.: 33

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.623 AC: 94814 AN: 152088 Hom.: 30340 Cov.: 33 AF XY: 0.631 AC XY: 46917 AN XY: 74358

African (AFR) AF: 0.472 AC: 19548 AN: 41440

American (AMR) AF: 0.674 AC: 10315 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2258 AN: 3472

East Asian (EAS) AF: 0.742 AC: 3822 AN: 5154

South Asian (SAS) AF: 0.603 AC: 2913 AN: 4830

European-Finnish (FIN) AF: 0.772 AC: 8170 AN: 10582

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45847 AN: 67988

Other (OTH) AF: 0.627 AC: 1322 AN: 2110

Alfa AF: 0.655 Hom.: 102897

Bravo AF: 0.610

Asia WGS AF: 0.685 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.65
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs9841212; hg19: chr3-134191938;