chr4-158269138-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000286558 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666585.1. 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
	ENSG00000286558	ENST00000666585.1		n.1320-927C>T		intron	N/A
	ENSG00000250604	ENST00000803056.1		n.336+34986G>A		intron	N/A
	ENSG00000250604	ENST00000803057.1		n.242+34986G>A		intron	N/A

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

African (AFR) AF: 0.288 AC: 11935 AN: 41450

American (AMR) AF: 0.588 AC: 8969 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1866 AN: 3470

East Asian (EAS) AF: 0.768 AC: 3941 AN: 5130

South Asian (SAS) AF: 0.712 AC: 3428 AN: 4816

European-Finnish (FIN) AF: 0.487 AC: 5132 AN: 10542

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35018 AN: 67912

Other (OTH) AF: 0.484 AC: 1020 AN: 2108

Alfa AF: 0.506 Hom.: 33746

Bravo AF: 0.471

Asia WGS AF: 0.725 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.77
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs1328925; hg19: chr4-159190290;