12-114009055-G-A

Position:

• chr12-114009055-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 0.354 in 152,052 control chromosomes in the GnomAD database, including 9,630 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 0.35 (9630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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: 0.354 AC: 53732 AN: 151934 Hom.: 9624 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.354 AC: 53771 AN: 152052 Hom.: 9630 Cov.: 32 AF XY: 0.353 AC XY: 26210 AN XY: 74344

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.358

Alfa AF: 0.365 Hom.: 13947

Bravo AF: 0.354

Asia WGS AF: 0.372 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12313095; hg19: chr12-114446860;