ENST00000751991.1:n.856C>T

Variant names:

• chr2-37796082-G-A
• rs4143271
• ENST00000751991.1:n.856C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000751991.1(PIRAT1):​n.856C>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 0.0956 in 152,130 control chromosomes in the GnomAD database, including 932 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 0.096 (932 hom., cov: 32)
• Consequence: PIRAT1 ENST00000751991.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74
• Publications: 1 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIRAT1	ENST00000751991.1	n.856C>T		non_coding_transcript_exon_variant	Exon 5 of 7
PIRAT1	ENST00000751992.1	n.609C>T		non_coding_transcript_exon_variant	Exon 4 of 6
PIRAT1	ENST00000751993.1	n.613C>T		non_coding_transcript_exon_variant	Exon 4 of 6

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14550 AN: 152012 Hom.: 932 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0944

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

GnomAD4 genome AF: 0.0956 AC: 14547 AN: 152130 Hom.: 932 Cov.: 32 AF XY: 0.101 AC XY: 7499 AN XY: 74360

African (AFR) AF: 0.0291 AC: 1210 AN: 41534

American (AMR) AF: 0.114 AC: 1746 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 425 AN: 3466

East Asian (EAS) AF: 0.288 AC: 1486 AN: 5162

South Asian (SAS) AF: 0.145 AC: 702 AN: 4826

European-Finnish (FIN) AF: 0.153 AC: 1611 AN: 10560

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7018 AN: 67982

Other (OTH) AF: 0.0935 AC: 197 AN: 2108

Alfa AF: 0.106 Hom.: 356

Bravo AF: 0.0890

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
DANN	Benign	0.80
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs4143271; hg19: chr2-38023225;