rs2220321

Positions:

• chr8-126899351-G-A

Variant summary

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

The ENST00000519319.2(PCAT1):​n.262+20871G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,168 control chromosomes in the GnomAD database, including 15,028 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 0.44 (15028 hom., cov: 32)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

PCAT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.663+21561G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.262+20871G>A		intron_variant		2
PCAT1	ENST00000643079.1	n.9+20871G>A		intron_variant
PCAT1	ENST00000643101.1	n.161+21561G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66370 AN: 151052 Hom.: 15012 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.635

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.439 AC: 66435 AN: 151168 Hom.: 15028 Cov.: 32 AF XY: 0.441 AC XY: 32557 AN XY: 73874

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.444

Alfa AF: 0.466 Hom.: 2084

Bravo AF: 0.423

Asia WGS AF: 0.425 AC: 1476 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2220321; hg19: chr8-127911596;