chr12-54697497-A-T

Variant names:

• chr12-54697497-A-T
• rs10506330

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 0.0621 in 152,268 control chromosomes in the GnomAD database, including 478 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 0.062 (478 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 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: 0.0621 AC: 9447 AN: 152150 Hom.: 477 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.0163

Gnomad SAS AF: 0.0668

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0311

Gnomad OTH AF: 0.0530

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

GnomAD4 genome AF: 0.0621 AC: 9458 AN: 152268 Hom.: 478 Cov.: 32 AF XY: 0.0612 AC XY: 4556 AN XY: 74472

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.0439

Gnomad4 ASJ AF: 0.0545

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.0669

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0311

Gnomad4 OTH AF: 0.0534

Alfa AF: 0.0490 Hom.: 50

Bravo AF: 0.0655

Asia WGS AF: 0.0580 AC: 202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506330; hg19: chr12-55091281;