4-53868344-T-C

Variant names:

• chr4-53868344-T-C
• rs1391758
• ENST00000507166.5:c.1018-406581T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507166.5(ENSG00000282278):​c.1018-406581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 151,926 control chromosomes in the GnomAD database, including 55,115 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 0.84 (55115 hom., cov: 29)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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.1018-406581T>C		intron_variant	Intron 12 of 23	2		ENSP00000423325.1

Frequencies

GnomAD3 genomes AF: 0.843 AC: 127980 AN: 151810 Hom.: 55082 Cov.: 29

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.843 AC: 128061 AN: 151926 Hom.: 55115 Cov.: 29 AF XY: 0.848 AC XY: 62946 AN XY: 74262

African (AFR) AF: 0.643 AC: 26574 AN: 41308

American (AMR) AF: 0.916 AC: 13989 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3082 AN: 3470

East Asian (EAS) AF: 0.979 AC: 5060 AN: 5170

South Asian (SAS) AF: 0.900 AC: 4329 AN: 4812

European-Finnish (FIN) AF: 0.969 AC: 10240 AN: 10572

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 62034 AN: 68012

Other (OTH) AF: 0.862 AC: 1815 AN: 2106

Alfa AF: 0.893 Hom.: 116820

Bravo AF: 0.831

Asia WGS AF: 0.928 AC: 3226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.39
PhyloP100		-0.42
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: rs1391758; hg19: chr4-54734511;