6-33129837-C-A

Variant names:

• chr6-33129837-C-A
• rs3129269

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;