8-142821403-C-T

Variant names:

• chr8-142821403-C-T
• rs12546765

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 0.357 in 152,064 control chromosomes in the GnomAD database, including 10,815 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 (10815 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.444 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: 0.357 AC: 54218 AN: 151946 Hom.: 10808 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.0995

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.357 AC: 54260 AN: 152064 Hom.: 10815 Cov.: 33 AF XY: 0.353 AC XY: 26239 AN XY: 74314

African (AFR) AF: 0.220 AC: 9125 AN: 41482

American (AMR) AF: 0.301 AC: 4601 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1671 AN: 3466

East Asian (EAS) AF: 0.0998 AC: 516 AN: 5172

South Asian (SAS) AF: 0.328 AC: 1582 AN: 4824

European-Finnish (FIN) AF: 0.455 AC: 4811 AN: 10564

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30485 AN: 67960

Other (OTH) AF: 0.362 AC: 764 AN: 2110

Alfa AF: 0.413 Hom.: 2107

Bravo AF: 0.334

Asia WGS AF: 0.230 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.80
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs12546765; hg19: chr8-143902819;