6-32224330-C-G

Variant names:

• chr6-32224330-C-G
• rs3134929

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 0.267 in 152,160 control chromosomes in the GnomAD database, including 6,308 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 0.27 (6308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 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: 0.267 AC: 40613 AN: 152042 Hom.: 6305 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.267 AC: 40634 AN: 152160 Hom.: 6308 Cov.: 32 AF XY: 0.262 AC XY: 19521 AN XY: 74408

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.0741

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.295

Alfa AF: 0.0890 Hom.: 102

Bravo AF: 0.289

Asia WGS AF: 0.370 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3134929; hg19: chr6-32192107; COSMIC: COSV66684196;