rs12658558
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138379.3(TIMD4):c.58+2501G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0285 in 152,192 control chromosomes in the GnomAD database, including 188 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 0.028 ( 188 hom., cov: 31)
Consequence
TIMD4
NM_138379.3 intron
NM_138379.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.34
Genes affected
TIMD4 (HGNC:25132): (T cell immunoglobulin and mucin domain containing 4) Predicted to enable phosphatidylserine binding activity. Predicted to act upstream of or within apoptotic cell clearance. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.98).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TIMD4 | NM_138379.3 | c.58+2501G>A | intron_variant | ENST00000274532.7 | |||
TIMD4 | NM_001146726.2 | c.58+2501G>A | intron_variant | ||||
TIMD4 | XM_011534694.3 | c.58+2501G>A | intron_variant | ||||
TIMD4 | XM_017010021.2 | c.58+2501G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TIMD4 | ENST00000274532.7 | c.58+2501G>A | intron_variant | 1 | NM_138379.3 | P2 | |||
TIMD4 | ENST00000407087.4 | c.58+2501G>A | intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0285 AC: 4328AN: 152074Hom.: 185 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0285 AC: 4333AN: 152192Hom.: 188 Cov.: 31 AF XY: 0.0315 AC XY: 2347AN XY: 74396
GnomAD4 genome
?
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4333
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152192
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31
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2347
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74396
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Asia WGS
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189
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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