rs12480887
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_052951.3(DNTTIP1):c.373-2295A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,250 control chromosomes in the GnomAD database, including 1,002 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 0.11 ( 1002 hom., cov: 32)
Consequence
DNTTIP1
NM_052951.3 intron
NM_052951.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.594
Genes affected
DNTTIP1 (HGNC:16160): (deoxynucleotidyltransferase terminal interacting protein 1) DNTTIP1 binds DNA and enhances the activity of terminal deoxynucleotidyltransferase (TDT, or DNTT; MIM 187410), a DNA polymerase that catalyzes the polymerization of DNA in the absence of a DNA template (Yamashita et al., 2001 [PubMed 11473582]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNTTIP1 | NM_052951.3 | c.373-2295A>G | intron_variant | ENST00000372622.8 | |||
DNTTIP1 | XM_024451823.2 | c.253-2295A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNTTIP1 | ENST00000372622.8 | c.373-2295A>G | intron_variant | 1 | NM_052951.3 | P1 | |||
DNTTIP1 | ENST00000415790.5 | c.253-2295A>G | intron_variant | 3 | |||||
DNTTIP1 | ENST00000435014.1 | c.153-2295A>G | intron_variant | 5 | |||||
DNTTIP1 | ENST00000456939.5 | c.224-2295A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.109 AC: 16543AN: 152132Hom.: 1006 Cov.: 32
GnomAD3 genomes
?
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16543
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152132
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.109 AC: 16545AN: 152250Hom.: 1002 Cov.: 32 AF XY: 0.111 AC XY: 8279AN XY: 74442
GnomAD4 genome
?
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AC:
16545
AN:
152250
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32
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8279
AN XY:
74442
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Asia WGS
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393
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at