rs3129963

Variant names:

• chr6-32412431-A-G
• rs3129963

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 0.163 in 152,188 control chromosomes in the GnomAD database, including 2,167 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 0.16 (2167 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 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: 0.163 AC: 24769 AN: 152070 Hom.: 2167 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0584

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.163 AC: 24781 AN: 152188 Hom.: 2167 Cov.: 32 AF XY: 0.158 AC XY: 11748 AN XY: 74412

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0584

Gnomad4 SAS AF: 0.0593

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.148

Alfa AF: 0.172 Hom.: 1460

Bravo AF: 0.157

Asia WGS AF: 0.0780 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129963; hg19: chr6-32380208;