12-126531637-A-G

Position:

• chr12-126531637-A-G

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 0.671 in 152,036 control chromosomes in the GnomAD database, including 37,011 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 0.67 (37011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101981 AN: 151918 Hom.: 36995 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.671 AC: 102038 AN: 152036 Hom.: 37011 Cov.: 32 AF XY: 0.679 AC XY: 50458 AN XY: 74322

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.677

Alfa AF: 0.748 Hom.: 40161

Bravo AF: 0.655

Asia WGS AF: 0.854 AC: 2965 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215396; hg19: chr12-127016183;