chr8-126970374-G-A

Position:

• chr8-126970374-G-A

Variant summary

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

The ENST00000519319.2(PCAT1):​n.263-36181G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,922 control chromosomes in the GnomAD database, including 5,242 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 0.24 (5242 hom., cov: 31)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794

Genes affected

PCAT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.664-36181G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.263-36181G>A		intron_variant		2
PCAT1	ENST00000643079.1	n.10-36181G>A		intron_variant
PCAT1	ENST00000643101.1	n.162-36181G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36255 AN: 151804 Hom.: 5237 Cov.: 31

Gnomad AFR AF: 0.0780

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.239 AC: 36259 AN: 151922 Hom.: 5242 Cov.: 31 AF XY: 0.246 AC XY: 18250 AN XY: 74240

Gnomad4 AFR AF: 0.0778

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.242

Alfa AF: 0.252 Hom.: 693

Bravo AF: 0.225

Asia WGS AF: 0.315 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1386468; hg19: chr8-127982619;