rs12546801

Variant names:

• chr8-142821552-C-T
• rs12546801

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.198 AC: 8232 AN: 41528

American (AMR) AF: 0.302 AC: 4621 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1661 AN: 3470

East Asian (EAS) AF: 0.150 AC: 775 AN: 5176

South Asian (SAS) AF: 0.325 AC: 1566 AN: 4816

European-Finnish (FIN) AF: 0.519 AC: 5487 AN: 10576

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30758 AN: 67960

Other (OTH) AF: 0.362 AC: 764 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.38
PhyloP100		-0.88

Splicing

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

Other links and lift over

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