rs10206788

Variant names:

• chr2-37829260-A-G
• rs10206788
• ENST00000413792.5:n.173T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-37829260-A-G
• chr2-37829260-A-T

Variant summary

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

The ENST00000413792.5(PIRAT1):​n.173T>C 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 0.593 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 ENST00000413792.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• 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=-0.93).
• 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 rank	MANE	Protein	UniProt
PIRAT1	NR_110011.1	n.452T>C		non_coding_transcript_exon_variant	Exon 1 of 3
PIRAT1	NR_110012.1	n.287-222T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIRAT1	ENST00000413792.5	n.173T>C		non_coding_transcript_exon_variant	Exon 1 of 3	2
PIRAT1	ENST00000655948.2	n.170T>C		non_coding_transcript_exon_variant	Exon 1 of 2
PIRAT1	ENST00000752005.1	n.140T>C		non_coding_transcript_exon_variant	Exon 1 of 4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.722 AC: 13 AN: 18

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.481 AC: 19974 AN: 41484

American (AMR) AF: 0.652 AC: 9971 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1994 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1534 AN: 5160

South Asian (SAS) AF: 0.501 AC: 2413 AN: 4820

European-Finnish (FIN) AF: 0.625 AC: 6600 AN: 10564

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.671 AC: 45628 AN: 67950

Other (OTH) AF: 0.588 AC: 1242 AN: 2112

Alfa AF: 0.645 Hom.: 53235

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10206788; hg19: chr2-38056403;