rs13239597

Positions:

• chr7-129055929-C-A

Variant summary

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

The NR_002187.3(TPI1P2):​n.707C>A 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 0.109 in 646,794 control chromosomes in the GnomAD database, including 4,747 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 0.090 (854 hom., cov: 32)
  • Exomes 𝑓: 0.11 (3893 hom.)
• Consequence: TPI1P2 NR_002187.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

TPI1P2 (HGNC:38069): (triosephosphate isomerase 1 pseudogene 2)

TNPO3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TPI1P2	NR_002187.3	n.707C>A		non_coding_transcript_exon_variant	1/1
TNPO3	XM_047420091.1	c.-240+66G>T		intron_variant			XP_047276047.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TPI1P2	ENST00000635637.1	n.707C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0902 AC: 13725 AN: 152200 Hom.: 857 Cov.: 32

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.102

GnomAD4 exome AF: 0.114 AC: 56551 AN: 494476 Hom.: 3893 Cov.: 4 AF XY: 0.116 AC XY: 30605 AN XY: 264160

Gnomad4 AFR exome AF: 0.0243

Gnomad4 AMR exome AF: 0.185

Gnomad4 ASJ exome AF: 0.113

Gnomad4 EAS exome AF: 0.000159

Gnomad4 SAS exome AF: 0.159

Gnomad4 FIN exome AF: 0.148

Gnomad4 NFE exome AF: 0.112

Gnomad4 OTH exome AF: 0.112

GnomAD4 genome AF: 0.0901 AC: 13719 AN: 152318 Hom.: 854 Cov.: 32 AF XY: 0.0927 AC XY: 6900 AN XY: 74472

Gnomad4 AFR AF: 0.0241

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.101

Alfa AF: 0.105 Hom.: 225

Bravo AF: 0.0864

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13239597; hg19: chr7-128695983;