chr2-37839573-T-C

Variant names:

• chr2-37839573-T-C
• rs7598641
• ENST00000418746.2:n.629+387A>G

Variant summary

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

The ENST00000446799.7(PIRAT1):​n.307-10535A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,646 control chromosomes in the GnomAD database, including 5,042 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 0.25 (5042 hom., cov: 33)
• Consequence: PIRAT1 ENST00000446799.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIRAT1	NR_110012.1	n.287-10535A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIRAT1	ENST00000418746.2	n.629+387A>G		intron_variant	Intron 3 of 3	4
PIRAT1	ENST00000446799.7	n.307-10535A>G		intron_variant	Intron 2 of 3	3
PIRAT1	ENST00000655678.1	n.454-18932A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38612 AN: 151528 Hom.: 5038 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.255 AC: 38639 AN: 151646 Hom.: 5042 Cov.: 33 AF XY: 0.256 AC XY: 18988 AN XY: 74070

African (AFR) AF: 0.239 AC: 9888 AN: 41308

American (AMR) AF: 0.199 AC: 3033 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1212 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1103 AN: 5154

South Asian (SAS) AF: 0.352 AC: 1687 AN: 4792

European-Finnish (FIN) AF: 0.283 AC: 2968 AN: 10474

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17841 AN: 67878

Other (OTH) AF: 0.273 AC: 574 AN: 2106

Alfa AF: 0.260 Hom.: 21959

Bravo AF: 0.242

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.94
DANN	Benign	0.44
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7598641; hg19: chr2-38066716;