12-54705212-T-A

Position:

• chr12-54705212-T-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 0.763 in 152,096 control chromosomes in the GnomAD database, including 44,495 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 0.76 (44495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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: 0.763 AC: 115989 AN: 151978 Hom.: 44434 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.763 AC: 116108 AN: 152096 Hom.: 44495 Cov.: 32 AF XY: 0.766 AC XY: 56955 AN XY: 74362

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.770

Alfa AF: 0.754 Hom.: 24035

Bravo AF: 0.776

Asia WGS AF: 0.880 AC: 3059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1153188; hg19: chr12-55098996;