chr12-68254396-A-T

Position:

• chr12-68254396-A-T

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 0.531 in 151,154 control chromosomes in the GnomAD database, including 21,623 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 0.53 (21623 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.575 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: 0.531 AC: 80264 AN: 151046 Hom.: 21620 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.531 AC: 80288 AN: 151154 Hom.: 21623 Cov.: 31 AF XY: 0.527 AC XY: 38872 AN XY: 73764

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.488

Alfa AF: 0.571 Hom.: 3104

Bravo AF: 0.526

Asia WGS AF: 0.401 AC: 1380 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2227483; hg19: chr12-68648176;