chr3-134437220-T-C

Variant names:

• chr3-134437220-T-C
• rs9829637

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 0.331 in 152,162 control chromosomes in the GnomAD database, including 8,719 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 0.33 (8719 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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: 0.331 AC: 50298 AN: 152044 Hom.: 8699 Cov.: 33

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0913

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.331 AC: 50348 AN: 152162 Hom.: 8719 Cov.: 33 AF XY: 0.326 AC XY: 24251 AN XY: 74390

African (AFR) AF: 0.310 AC: 12870 AN: 41524

American (AMR) AF: 0.314 AC: 4795 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3468

East Asian (EAS) AF: 0.0906 AC: 470 AN: 5188

South Asian (SAS) AF: 0.177 AC: 854 AN: 4832

European-Finnish (FIN) AF: 0.350 AC: 3707 AN: 10590

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25270 AN: 67970

Other (OTH) AF: 0.330 AC: 694 AN: 2106

Alfa AF: 0.359 Hom.: 1244

Bravo AF: 0.332

Asia WGS AF: 0.125 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.86
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs9829637; hg19: chr3-134156062;