rs9532645

chr13-40880898-G-Achr13-40880898-G-C

Variant summary

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

The NR_038259.1(TPTE2P5):n.133-25083C>T 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 0.536 in 152,082 control chromosomes in the GnomAD database, including 25,325 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 0.54 (25325 hom., cov: 32)
• Consequence: TPTE2P5 NR_038259.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPTE2P5	NR_038259.1	n.133-25083C>T		intron_variant, non_coding_transcript_variant
TPTE2P5	NR_038258.1	n.133-25083C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652519.1	n.176+27261C>T		intron_variant, non_coding_transcript_variant
	ENST00000379515.3	n.132-25083C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000633547.1	n.152-25083C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81504 AN: 151964 Hom.: 25337 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.536 AC: 81498 AN: 152082 Hom.: 25325 Cov.: 32 AF XY: 0.541 AC XY: 40211 AN XY: 74354

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.565

Alfa AF: 0.660 Hom.: 32414

Bravo AF: 0.520

Asia WGS AF: 0.348 AC: 1210 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	0.79
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9532645; hg19: chr13-41455034; COSMIC: COSV65346936;