4-54145602-T-C

Position:

• chr4-54145602-T-C

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1018-129323T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,052 control chromosomes in the GnomAD database, including 42,094 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 0.74 (42094 hom., cov: 31)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

ENSG00000282278 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54145602T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000282278	ENST00000507166.5	c.1018-129323T>C		intron_variant		2		ENSP00000423325.1

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111923 AN: 151934 Hom.: 42070 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.737 AC: 111990 AN: 152052 Hom.: 42094 Cov.: 31 AF XY: 0.738 AC XY: 54846 AN XY: 74308

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.743

Alfa AF: 0.757 Hom.: 18685

Bravo AF: 0.735

Asia WGS AF: 0.807 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1364989; hg19: chr4-55011769;