4-79852307-C-T

Variant names:

• chr4-79852307-C-T
• rs6857026
• ENST00000504263.2:n.282-8983C>T

Variant summary

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

The ENST00000504263.2(PCAT4):​n.282-8983C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,878 control chromosomes in the GnomAD database, including 8,053 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 0.32 (8053 hom., cov: 32)
• Consequence: PCAT4 ENST00000504263.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997
• Publications: 4 publications found

Genes affected

PCAT4 (HGNC:24853): (prostate cancer associated transcript 4)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504263.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT4	NR_026555.1		n.134-8983C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCAT4	ENST00000504263.2	TSL:1	n.282-8983C>T		intron	N/A
	PCAT4	ENST00000514836.1	TSL:3	n.70-8983C>T		intron	N/A
	PCAT4	ENST00000775423.1		n.102-8983C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48747 AN: 151760 Hom.: 8045 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.321 AC: 48786 AN: 151878 Hom.: 8053 Cov.: 32 AF XY: 0.326 AC XY: 24179 AN XY: 74202

African (AFR) AF: 0.343 AC: 14197 AN: 41406

American (AMR) AF: 0.304 AC: 4637 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1084 AN: 3468

East Asian (EAS) AF: 0.269 AC: 1384 AN: 5140

South Asian (SAS) AF: 0.536 AC: 2576 AN: 4806

European-Finnish (FIN) AF: 0.334 AC: 3524 AN: 10548

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20418 AN: 67950

Other (OTH) AF: 0.323 AC: 681 AN: 2106

Alfa AF: 0.303 Hom.: 21631

Bravo AF: 0.311

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.5
DANN	Benign	0.67
PhyloP100		1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6857026;

hg19: chr4-80773461;