4-54145602-T-C

Variant names:

• chr4-54145602-T-C
• rs1364989
• ENST00000507166.5:c.1018-129323T>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282278	ENST00000507166.5	c.1018-129323T>C		intron_variant	Intron 12 of 23	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;