chr4-54145602-T-C

Variant names:

• chr4-54145602-T-C
• rs1364989
• ENST00000507166.5:c.1018-129323T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

ENSG00000282278 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507166.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282278	ENST00000507166.5	TSL:2	c.1018-129323T>C		intron	N/A	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

African (AFR) AF: 0.590 AC: 24466 AN: 41470

American (AMR) AF: 0.811 AC: 12381 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2621 AN: 3470

East Asian (EAS) AF: 0.954 AC: 4933 AN: 5172

South Asian (SAS) AF: 0.724 AC: 3484 AN: 4810

European-Finnish (FIN) AF: 0.776 AC: 8194 AN: 10564

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53347 AN: 67980

Other (OTH) AF: 0.743 AC: 1568 AN: 2110

Alfa AF: 0.758 Hom.: 21197

Bravo AF: 0.735

Asia WGS AF: 0.807 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.72
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1364989; hg19: chr4-55011769;