rs979200

Positions:

• chr8-126911475-C-T

Variant summary

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

The ENST00000519319.2(PCAT1):​n.262+32995C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,070 control chromosomes in the GnomAD database, including 16,767 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 0.45 (16767 hom., cov: 32)
• Consequence: PCAT1 ENST00000519319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

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 (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375751	NR_188069.1	n.663+33685C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCAT1	ENST00000519319.2	n.262+32995C>T		intron_variant		2
PCAT1	ENST00000643079.1	n.9+32995C>T		intron_variant
PCAT1	ENST00000643101.1	n.161+33685C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67890 AN: 151952 Hom.: 16751 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.447 AC: 67940 AN: 152070 Hom.: 16767 Cov.: 32 AF XY: 0.441 AC XY: 32768 AN XY: 74320

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.465

Alfa AF: 0.381 Hom.: 16660

Bravo AF: 0.472

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs979200; hg19: chr8-127923720;