13-24959693-A-T

Variant names:

• chr13-24959693-A-T
• rs2483374
• ENST00000429698.3:n.297-8205T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000429698.3(ENSG00000291041):​n.297-8205T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000381 in 262,184 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000038 (0 hom.)
• Consequence: ENSG00000291041 ENST00000429698.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 5 publications found

Genes affected

ENSG00000291041 (HGNC:):

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429698.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TPTE2P1	NR_026730.2		n.280-8205T>A		intron	N/A
	TPTE2P1	NR_178209.1		n.280-8205T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291041	ENST00000429698.3	TSL:3	n.297-8205T>A		intron	N/A
	ENSG00000291041	ENST00000434100.5	TSL:3	n.134+7699T>A		intron	N/A
	TPTE2P1	ENST00000435256.1	TSL:6	n.329+41T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000381 AC: 1 AN: 262184 Hom.: 0 Cov.: 5 AF XY: 0.00000725 AC XY: 1 AN XY: 137966

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 5346

American (AMR) AF: 0.00 AC: 0 AN: 4738

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4842

East Asian (EAS) AF: 0.00 AC: 0 AN: 5796

South Asian (SAS) AF: 0.00 AC: 0 AN: 14626

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21990

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 840

European-Non Finnish (NFE) AF: 0.00000519 AC: 1 AN: 192560

Other (OTH) AF: 0.00 AC: 0 AN: 11446

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 48951

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.8
DANN	Benign	0.15
PhyloP100		-0.66

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2483374;

hg19: chr13-25533831;