rs329134

chr3-138035711-C-T

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 0.362 in 152,004 control chromosomes in the GnomAD database, including 11,470 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 0.36 (11470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 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: 0.362 AC: 54962 AN: 151886 Hom.: 11480 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.362 AC: 54950 AN: 152004 Hom.: 11470 Cov.: 32 AF XY: 0.355 AC XY: 26358 AN XY: 74274

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.404

Alfa AF: 0.454 Hom.: 7439

Bravo AF: 0.351

Asia WGS AF: 0.327 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.7
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs329134; hg19: chr3-137754553;