rs10495875

chr2-37827954-G-A

Variant summary

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

The NR_110012.1(PIRAT1):n.393-76C>T variant causes a intron, non coding transcript 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 NR_110012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PIRAT1	NR_110012.1	n.393-76C>T		intron_variant, non_coding_transcript_variant
PIRAT1	NR_110011.1	n.571-76C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIRAT1	ENST00000655678.1	n.454-7313C>T		intron_variant, non_coding_transcript_variant
PIRAT1	ENST00000413792.5	n.292-76C>T		intron_variant, non_coding_transcript_variant		2
PIRAT1	ENST00000446799.6	n.393-76C>T		intron_variant, non_coding_transcript_variant		3
PIRAT1	ENST00000655948.1	n.470-76C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.218

Gnomad4 AMR exome AF: 0.0598

Gnomad4 ASJ exome AF: 0.141

Gnomad4 EAS exome AF: 0.0781

Gnomad4 SAS exome AF: 0.0796

Gnomad4 FIN exome AF: 0.0999

Gnomad4 NFE exome AF: 0.0838

Gnomad4 OTH exome AF: 0.100

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

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.0731

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0918

Gnomad4 SAS AF: 0.0851

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0815

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0860 Hom.: 591

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495875; hg19: chr2-38055097;