chr3-134304214-T-C

Variant names:

• chr3-134304214-T-C
• rs9843732

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 0.314 in 152,170 control chromosomes in the GnomAD database, including 8,589 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 0.31 (8589 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.851
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47724 AN: 152052 Hom.: 8576 Cov.: 34

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.314 AC: 47773 AN: 152170 Hom.: 8589 Cov.: 34 AF XY: 0.320 AC XY: 23813 AN XY: 74396

African (AFR) AF: 0.266 AC: 11039 AN: 41512

American (AMR) AF: 0.362 AC: 5535 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 790 AN: 3468

East Asian (EAS) AF: 0.860 AC: 4450 AN: 5176

South Asian (SAS) AF: 0.427 AC: 2058 AN: 4822

European-Finnish (FIN) AF: 0.279 AC: 2955 AN: 10586

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19942 AN: 68000

Other (OTH) AF: 0.309 AC: 654 AN: 2114

Alfa AF: 0.301 Hom.: 4616

Bravo AF: 0.321

Asia WGS AF: 0.629 AC: 2186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.9
DANN	Benign	0.62
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs9843732; hg19: chr3-134023056;