rs1256531

Variant names:

• chr14-65281041-A-G
• rs1256531
• ENST00000554374.2:n.1476A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

Genes affected

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

ENSG00000305690 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PTBP1P		n.65281041A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTBP1P	ENST00000554374.2	n.1476A>G		non_coding_transcript_exon_variant	Exon 2 of 2	6
ENSG00000305690	ENST00000812438.1	n.1782A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000258760	ENST00000553754.1	n.301-11529T>C		intron_variant	Intron 1 of 2	4
ENSG00000258760	ENST00000555736.1	n.152+21488T>C		intron_variant	Intron 1 of 3	5

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

African (AFR) AF: 0.538 AC: 12215 AN: 22722

American (AMR) AF: 0.150 AC: 5743 AN: 38232

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 3674 AN: 19762

East Asian (EAS) AF: 0.203 AC: 7515 AN: 37020

South Asian (SAS) AF: 0.222 AC: 14942 AN: 67388

European-Finnish (FIN) AF: 0.117 AC: 5724 AN: 49116

Middle Eastern (MID) AF: 0.131 AC: 526 AN: 4014

European-Non Finnish (NFE) AF: 0.0884 AC: 57645 AN: 652300

Other (OTH) AF: 0.149 AC: 6300 AN: 42188

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

African (AFR) AF: 0.523 AC: 21699 AN: 41458

American (AMR) AF: 0.189 AC: 2886 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 623 AN: 3472

East Asian (EAS) AF: 0.198 AC: 1023 AN: 5168

South Asian (SAS) AF: 0.234 AC: 1128 AN: 4818

European-Finnish (FIN) AF: 0.119 AC: 1263 AN: 10602

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0969 AC: 6585 AN: 67990

Other (OTH) AF: 0.199 AC: 419 AN: 2108

Alfa AF: 0.139 Hom.: 11300

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
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs1256531; hg19: chr14-65747759;