8-126999692-T-C

Position:

• chr8-126999692-T-C

Variant summary

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

The ENST00000519319.2(PCAT1):​n.263-6863T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,998 control chromosomes in the GnomAD database, including 6,006 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 0.28 (6006 hom., cov: 32)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

PCAT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.664-6863T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.263-6863T>C		intron_variant		2
PCAT1	ENST00000643079.1	n.10-6863T>C		intron_variant
PCAT1	ENST00000643101.1	n.162-6863T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41968 AN: 151880 Hom.: 5990 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.276 AC: 42012 AN: 151998 Hom.: 6006 Cov.: 32 AF XY: 0.275 AC XY: 20410 AN XY: 74282

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.302

Alfa AF: 0.296 Hom.: 13732

Bravo AF: 0.282

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10086908; hg19: chr8-128011937;