8-20374603-T-C

Position:

• chr8-20374603-T-C

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 0.351 in 151,962 control chromosomes in the GnomAD database, including 10,653 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 0.35 (10653 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20374603T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53219 AN: 151842 Hom.: 10644 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.351 AC: 53263 AN: 151962 Hom.: 10653 Cov.: 31 AF XY: 0.360 AC XY: 26757 AN XY: 74268

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.351

Alfa AF: 0.351 Hom.: 1268

Bravo AF: 0.335

Asia WGS AF: 0.578 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
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: rs34393111; hg19: chr8-20232114;