rs1256531

chr14-65281041-A-G

Variant summary

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

The ENST00000554374.2(PTBP1P):n.1476A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.138 in 1,084,830 control chromosomes in the GnomAD database, including 17,279 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 0.23 (6824 hom., cov: 32)
  • Exomes 𝑓: 0.12 (10455 hom.)
• Consequence: PTBP1P ENST00000554374.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.95

Genes affected

PTBP1P (HGNC:20030): (polypyrimidine tract binding protein 1 pseudogene)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTBP1P	ENST00000554374.2	n.1476A>G		non_coding_transcript_exon_variant	2/2
	ENST00000555736.1	n.152+21488T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000553754.1	n.301-11529T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35636 AN: 151970 Hom.: 6782 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.196

GnomAD4 exome AF: 0.123 AC: 114284 AN: 932742 Hom.: 10455 Cov.: 12 AF XY: 0.125 AC XY: 59832 AN XY: 479828

Gnomad4 AFR exome AF: 0.538

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.186

Gnomad4 EAS exome AF: 0.203

Gnomad4 SAS exome AF: 0.222

Gnomad4 FIN exome AF: 0.117

Gnomad4 NFE exome AF: 0.0884

Gnomad4 OTH exome AF: 0.149

GnomAD4 genome AF: 0.235 AC: 35736 AN: 152088 Hom.: 6824 Cov.: 32 AF XY: 0.236 AC XY: 17575 AN XY: 74372

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0969

Gnomad4 OTH AF: 0.199

Alfa AF: 0.121 Hom.: 3516

Bravo AF: 0.251

Asia WGS AF: 0.311 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	12
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1256531; hg19: chr14-65747759;