rs3129269

Positions:

• chr6-33129837-C-A
• chr6-33129837-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 0.305 in 152,030 control chromosomes in the GnomAD database, including 7,306 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 (7306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 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: 0.305 AC: 46390 AN: 151914 Hom.: 7307 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.305 AC: 46407 AN: 152030 Hom.: 7306 Cov.: 32 AF XY: 0.307 AC XY: 22786 AN XY: 74290

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.311

Alfa AF: 0.324 Hom.: 8682

Bravo AF: 0.294

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129269; hg19: chr6-33097614;