ENST00000325407.4:n.189-10999G>T

Variant names:

• chr4-170592586-C-A
• rs368771
• ENST00000325407.4:n.189-10999G>T

Variant summary

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

The ENST00000325407.4(ENSG00000293021):​n.189-10999G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,020 control chromosomes in the GnomAD database, including 24,686 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 0.53 (24686 hom., cov: 32)
• Consequence: ENSG00000293021 ENST00000325407.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 3 publications found

Genes affected

ENSG00000293021 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000325407.4. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293021	ENST00000325407.4	TSL:1	n.189-10999G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80414 AN: 151902 Hom.: 24683 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.529 AC: 80442 AN: 152020 Hom.: 24686 Cov.: 32 AF XY: 0.537 AC XY: 39895 AN XY: 74306

African (AFR) AF: 0.217 AC: 8983 AN: 41484

American (AMR) AF: 0.455 AC: 6937 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2037 AN: 3470

East Asian (EAS) AF: 0.842 AC: 4348 AN: 5162

South Asian (SAS) AF: 0.676 AC: 3252 AN: 4812

European-Finnish (FIN) AF: 0.780 AC: 8245 AN: 10572

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44757 AN: 67954

Other (OTH) AF: 0.538 AC: 1136 AN: 2112

Alfa AF: 0.608 Hom.: 46856

Bravo AF: 0.493

Asia WGS AF: 0.743 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.71
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs368771; hg19: chr4-171513737;