4-158269138-C-T

Variant names:

• chr4-158269138-C-T
• rs1328925
• ENST00000666585.1:n.1320-927C>T

Variant summary

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

The ENST00000666585.1(ENSG00000286558):​n.1320-927C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,874 control chromosomes in the GnomAD database, including 18,409 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 0.47 (18409 hom., cov: 32)
• Consequence: ENSG00000286558 ENST00000666585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

Genes affected

ENSG00000286558 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 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
ENSG00000286558	ENST00000666585.1	n.1320-927C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72063 AN: 151756 Hom.: 18395 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.475 AC: 72096 AN: 151874 Hom.: 18409 Cov.: 32 AF XY: 0.481 AC XY: 35684 AN XY: 74200

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.484

Alfa AF: 0.512 Hom.: 27425

Bravo AF: 0.471

Asia WGS AF: 0.725 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328925; hg19: chr4-159190290;