rs10206788

chr2-37829260-A-Gchr2-37829260-A-T

Variant summary

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

The NR_110012.1(PIRAT1):n.287-222T>C 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 0.593 in 152,062 control chromosomes in the GnomAD database, including 27,427 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 0.59 (27423 hom., cov: 31)
  • Exomes 𝑓: 0.70 (4 hom.)
• Consequence: PIRAT1 NR_110012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIRAT1	NR_110012.1	n.287-222T>C		intron_variant, non_coding_transcript_variant
PIRAT1	NR_110011.1	n.452T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIRAT1	ENST00000655678.1	n.454-8619T>C		intron_variant, non_coding_transcript_variant
PIRAT1	ENST00000413792.5	n.173T>C		non_coding_transcript_exon_variant	1/3	2
PIRAT1	ENST00000655948.1	n.142T>C		non_coding_transcript_exon_variant	1/2
PIRAT1	ENST00000446799.6	n.287-222T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90086 AN: 151924 Hom.: 27419 Cov.: 31

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.591

GnomAD4 exome AF: 0.700 AC: 14 AN: 20 Hom.: 4 Cov.: 0 AF XY: 0.688 AC XY: 11 AN XY: 16

Gnomad4 NFE exome AF: 0.722

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.593 AC: 90126 AN: 152042 Hom.: 27423 Cov.: 31 AF XY: 0.589 AC XY: 43801 AN XY: 74330

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.588

Alfa AF: 0.650 Hom.: 43021

Bravo AF: 0.593

Asia WGS AF: 0.424 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	6.7
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10206788; hg19: chr2-38056403;