8-142821403-C-T

Position:

• chr8-142821403-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 0.357 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.142821403C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.0998

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.362

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12546765; hg19: chr8-143902819;