20-5360363-C-T

Variant names:

• chr20-5360363-C-T
• rs4813744
• ENST00000668553.1:n.1120+39191C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668553.1(ENSG00000266908):​n.1120+39191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000266908 ENST00000668553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

Genes affected

ENSG00000266908 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266908	ENST00000668553.1	n.1120+39191C>T		intron_variant	Intron 2 of 3

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;