rs1323855
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000299413.7(TRIM44):c.1007+11165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0148 in 152,020 control chromosomes in the GnomAD database, including 56 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 0.015 ( 56 hom., cov: 31)
Consequence
TRIM44
ENST00000299413.7 intron
ENST00000299413.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.151
Genes affected
TRIM44 (HGNC:19016): (tripartite motif containing 44) This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, namely a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. [provided by RefSeq, Jul 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=-0.83).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0148 (2246/152020) while in subpopulation AFR AF= 0.051 (2114/41466). AF 95% confidence interval is 0.0492. There are 56 homozygotes in gnomad4. There are 1056 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2246 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIM44 | NM_017583.6 | c.1007+11165C>T | intron_variant | ENST00000299413.7 | NP_060053.2 | |||
TRIM44 | XM_006718254.2 | c.767+11165C>T | intron_variant | XP_006718317.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM44 | ENST00000299413.7 | c.1007+11165C>T | intron_variant | 1 | NM_017583.6 | ENSP00000299413 | P1 | |||
TRIM44 | ENST00000532066.1 | n.373+11165C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0148 AC: 2241AN: 151906Hom.: 56 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0148 AC: 2246AN: 152020Hom.: 56 Cov.: 31 AF XY: 0.0142 AC XY: 1056AN XY: 74304
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ClinVar
Not reported inComputational scores
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Name
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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