chr12-130166709-G-A

Position:

• chr12-130166709-G-A

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 0.302 in 152,024 control chromosomes in the GnomAD database, including 7,654 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 0.30 (7654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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 (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45802 AN: 151906 Hom.: 7630 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.302 AC: 45863 AN: 152024 Hom.: 7654 Cov.: 32 AF XY: 0.309 AC XY: 22944 AN XY: 74306

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.284

Alfa AF: 0.270 Hom.: 1170

Bravo AF: 0.297

Asia WGS AF: 0.568 AC: 1979 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	0.65
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463865; hg19: chr12-130651254;