rs12546801

Variant names:

• chr8-142821552-C-T
• rs12546801

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 0.359 in 152,148 control chromosomes in the GnomAD database, including 11,083 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 0.36 (11083 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.359 AC: 54551 AN: 152028 Hom.: 11085 Cov.: 34

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.359 AC: 54553 AN: 152148 Hom.: 11083 Cov.: 34 AF XY: 0.358 AC XY: 26589 AN XY: 74364

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.362

Alfa AF: 0.415 Hom.: 1776

Bravo AF: 0.331

Asia WGS AF: 0.234 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12546801; hg19: chr8-143902968; COSMIC: COSV53509575;