20-5360363-C-T

Position:

• chr20-5360363-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 0.416 in 151,894 control chromosomes in the GnomAD database, including 13,330 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 0.42 (13330 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5360363C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266908	ENST00000668553.1	n.1120+39191C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63145 AN: 151776 Hom.: 13315 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.416 AC: 63205 AN: 151894 Hom.: 13330 Cov.: 32 AF XY: 0.416 AC XY: 30834 AN XY: 74200

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.443

Alfa AF: 0.373 Hom.: 1937

Bravo AF: 0.418

Asia WGS AF: 0.479 AC: 1663 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4813744; hg19: chr20-5341009;