rs12546801

Positions:

• chr8-142821552-C-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 0.359 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;