rs12529779

Variant names:

• chr6-137224969-A-G
• rs12529779

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 0.158 in 152,138 control chromosomes in the GnomAD database, including 2,131 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 (2131 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 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: 0.158 AC: 24036 AN: 152020 Hom.: 2131 Cov.: 31

Gnomad AFR AF: 0.0725

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.158 AC: 24027 AN: 152138 Hom.: 2131 Cov.: 31 AF XY: 0.157 AC XY: 11666 AN XY: 74382

Gnomad4 AFR AF: 0.0724

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.183

Alfa AF: 0.194 Hom.: 4015

Bravo AF: 0.155

Asia WGS AF: 0.146 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.61
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12529779; hg19: chr6-137546106;