rs12529779

Variant names:

• chr6-137224969-A-G
• rs12529779

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0724 AC: 3004 AN: 41494

American (AMR) AF: 0.173 AC: 2643 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3466

East Asian (EAS) AF: 0.196 AC: 1013 AN: 5170

South Asian (SAS) AF: 0.114 AC: 548 AN: 4820

European-Finnish (FIN) AF: 0.172 AC: 1816 AN: 10562

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13493 AN: 68010

Other (OTH) AF: 0.183 AC: 387 AN: 2110

Alfa AF: 0.189 Hom.: 5273

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs12529779; hg19: chr6-137546106;