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 ENST00000812438.1(ENSG00000305690):​n.1782A>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: ENSG00000305690 ENST00000812438.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812438.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTBP1P	ENST00000554374.2	TSL:6	n.1476A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000305690	ENST00000812438.1		n.1782A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000258760	ENST00000553754.1	TSL:4	n.301-11529T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1256531;

hg19: chr14-65747759;