rs329134

Variant names:

• chr3-138035711-C-T
• rs329134

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 0.362 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.155 AC: 6440 AN: 41482

American (AMR) AF: 0.347 AC: 5303 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1747 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1442 AN: 5164

South Asian (SAS) AF: 0.410 AC: 1972 AN: 4814

European-Finnish (FIN) AF: 0.353 AC: 3716 AN: 10534

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32816 AN: 67972

Other (OTH) AF: 0.404 AC: 849 AN: 2100

Alfa AF: 0.453 Hom.: 8330

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs329134; hg19: chr3-137754553;