rs10495875

Variant names:

• chr2-37827954-G-A
• rs10495875
• ENST00000752018.1:n.166C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000752018.1(PIRAT1):​n.166C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 396,140 control chromosomes in the GnomAD database, including 2,569 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 0.12 (1436 hom., cov: 34)
  • Exomes 𝑓: 0.091 (1133 hom.)
• Consequence: PIRAT1 ENST00000752018.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 6 publications found

Genes affected

PIRAT1 (HGNC:37459): (PU.1 (SPI1) induced regulator of S100A8 and S100A9 alarmin transcription 1)

CDC42EP3-AS1 (HGNC:56370): (CDC42EP3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIRAT1	NR_110011.1	n.571-76C>T		intron_variant	Intron 2 of 2
PIRAT1	NR_110012.1	n.393-76C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIRAT1	ENST00000752018.1	n.166C>T		non_coding_transcript_exon_variant	Exon 1 of 1
PIRAT1	ENST00000413792.5	n.292-76C>T		intron_variant	Intron 2 of 2	2
PIRAT1	ENST00000418746.2	n.630-76C>T		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18564 AN: 152146 Hom.: 1431 Cov.: 34

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0914

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.114

GnomAD4 exome AF: 0.0911 AC: 22222 AN: 243876 Hom.: 1133 AF XY: 0.0902 AC XY: 11156 AN XY: 123640

African (AFR) AF: 0.218 AC: 1551 AN: 7110

American (AMR) AF: 0.0598 AC: 441 AN: 7370

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 1297 AN: 9184

East Asian (EAS) AF: 0.0781 AC: 1781 AN: 22792

South Asian (SAS) AF: 0.0796 AC: 193 AN: 2426

European-Finnish (FIN) AF: 0.0999 AC: 2061 AN: 20628

Middle Eastern (MID) AF: 0.0969 AC: 124 AN: 1280

European-Non Finnish (NFE) AF: 0.0838 AC: 13148 AN: 156832

Other (OTH) AF: 0.100 AC: 1626 AN: 16254

GnomAD4 genome AF: 0.122 AC: 18604 AN: 152264 Hom.: 1436 Cov.: 34 AF XY: 0.121 AC XY: 8993 AN XY: 74466

African (AFR) AF: 0.219 AC: 9089 AN: 41536

American (AMR) AF: 0.0731 AC: 1119 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3472

East Asian (EAS) AF: 0.0918 AC: 476 AN: 5186

South Asian (SAS) AF: 0.0851 AC: 410 AN: 4820

European-Finnish (FIN) AF: 0.107 AC: 1139 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0815 AC: 5545 AN: 68022

Other (OTH) AF: 0.115 AC: 243 AN: 2114

Alfa AF: 0.0918 Hom.: 928

Bravo AF: 0.124

Asia WGS AF: 0.101 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.73
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10495875; hg19: chr2-38055097;