Genetic Variant ENST00000429698.3:n.297-8205T>A (chr13-24959693-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.664

Publications

5 publications found

Variant links:

Genes affected

ENSG00000291041 (HGNC:):

ENSG00000291041 links:

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

TPTE2P1 links:

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ACMG classification

Classification was made for transcript

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TPTE2P1	NR_026730.2 link	n.280-8205T>A		intron_variant	Intron 1 of 4
TPTE2P1	NR_178209.1 link	n.280-8205T>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000291041	ENST00000429698.3 link	n.297-8205T>A	intron_variant	Intron 1 of 6	3
ENSG00000291041	ENST00000434100.5 link	n.134+7699T>A	intron_variant	Intron 2 of 5	3
TPTE2P1	ENST00000435256.1 link	n.329+41T>A	intron_variant	Intron 4 of 6	6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000381

AC:

AN:

262184

Hom.:

Cov.:

AF XY:

0.00000725

AC XY:

AN XY:

137966

show subpopulations

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

African (AFR)

AF:

0.00

AC:

AN:

5346

American (AMR)

AF:

0.00

AC:

AN:

4738

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4842

East Asian (EAS)

AF:

0.00

AC:

AN:

5796

South Asian (SAS)

AF:

0.00

AC:

AN:

14626

European-Finnish (FIN)

AF:

0.00

AC:

AN:

21990

Middle Eastern (MID)

AF:

0.00

AC:

AN:

840

European-Non Finnish (NFE)

AF:

0.00000519

AC:

AN:

192560

Other (OTH)

AF:

0.00

AC:

AN:

11446

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.225

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

48951

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

5.8

(source)

DANN

Benign

0.15

PhyloP100

-0.66

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over