rs2483374

chr13-24959693-A-Cchr13-24959693-A-T

Variant summary

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

The NR_026730.2(TPTE2P1):n.280-8205T>G 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 0.495 in 412,964 control chromosomes in the GnomAD database, including 51,974 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 0.49 (19143 hom., cov: 32)
  • Exomes 𝑓: 0.50 (32831 hom.)
• Consequence: TPTE2P1 NR_026730.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664

Genes affected

TPTE2P1 (HGNC:35196): (TPTE2 pseudogene 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TPTE2P1	NR_026730.2	n.280-8205T>G		intron_variant, non_coding_transcript_variant
TPTE2P1	NR_178209.1	n.280-8205T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TPTE2P1	ENST00000435256.1	n.329+41T>G		intron_variant, non_coding_transcript_variant
	ENST00000690064.2	n.316-4824T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74998 AN: 151844 Hom.: 19120 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.506

GnomAD4 exome AF: 0.496 AC: 129559 AN: 261002 Hom.: 32831 Cov.: 5 AF XY: 0.502 AC XY: 68911 AN XY: 137346

Gnomad4 AFR exome AF: 0.601

Gnomad4 AMR exome AF: 0.384

Gnomad4 ASJ exome AF: 0.529

Gnomad4 EAS exome AF: 0.304

Gnomad4 SAS exome AF: 0.574

Gnomad4 FIN exome AF: 0.374

Gnomad4 NFE exome AF: 0.509

Gnomad4 OTH exome AF: 0.505

GnomAD4 genome AF: 0.494 AC: 75058 AN: 151962 Hom.: 19143 Cov.: 32 AF XY: 0.488 AC XY: 36274 AN XY: 74272

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.510

Alfa AF: 0.484 Hom.: 19407

Bravo AF: 0.499

Asia WGS AF: 0.445 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	6.1
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2483374; hg19: chr13-25533831;