8-126929548-G-A

Position:

• chr8-126929548-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000519319.2(PCAT1):​n.262+51068G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00406 in 152,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.0041 (0 hom., cov: 32)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -1.14

Genes affected

PCAT1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.663+51758G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.262+51068G>A		intron_variant		2
PCAT1	ENST00000643079.1	n.9+51068G>A		intron_variant
PCAT1	ENST00000643101.1	n.161+51758G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00407 AC: 619 AN: 152180 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00106

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00592

Gnomad OTH AF: 0.00191

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

GnomAD4 genome AF: 0.00406 AC: 619 AN: 152298 Hom.: 0 Cov.: 32 AF XY: 0.00424 AC XY: 316 AN XY: 74480

Gnomad4 AFR AF: 0.00106

Gnomad4 AMR AF: 0.00131

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.00592

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.00535 Hom.: 0

Bravo AF: 0.00301

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Familial prostate cancer Other:1

association, no assertion criteria provided

research

University of Washington Center for Mendelian Genomics, University of Washington

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs182352457; hg19: chr8-127941793;