rs17411119

Positions:

• chr2-37839540-T-C

Variant summary

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

The NR_110012.1(PIRAT1):​n.287-10502A>G 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 0.215 in 152,116 control chromosomes in the GnomAD database, including 3,860 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 0.21 (3860 hom., cov: 33)
• Consequence: PIRAT1 NR_110012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIRAT1	NR_110012.1	n.287-10502A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIRAT1	ENST00000655678.1	n.454-18899A>G		intron_variant, non_coding_transcript_variant
PIRAT1	ENST00000446799.6	n.287-10502A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32689 AN: 151998 Hom.: 3863 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.239

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.215 AC: 32689 AN: 152116 Hom.: 3860 Cov.: 33 AF XY: 0.217 AC XY: 16143 AN XY: 74342

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.239

Alfa AF: 0.248 Hom.: 6660

Bravo AF: 0.199

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17411119; hg19: chr2-38066683;