chr5-154457546-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_024632.6(SAP30L):c.*1518C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0197 in 152,244 control chromosomes in the GnomAD database, including 43 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 0.020 ( 43 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SAP30L
NM_024632.6 3_prime_UTR
NM_024632.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.64
Genes affected
SAP30L (HGNC:25663): (SAP30 like) Enables several functions, including non-sequence-specific DNA binding activity, bending; phosphatidylinositol phosphate binding activity; and zinc ion binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in fibrillar center and nucleoplasm. Part of histone deacetylase complex. [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=-0.87).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0197 (2993/152244) while in subpopulation SAS AF= 0.0429 (207/4822). AF 95% confidence interval is 0.0381. There are 43 homozygotes in gnomad4. There are 1442 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 43 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAP30L | NM_024632.6 | c.*1518C>T | 3_prime_UTR_variant | 4/4 | ENST00000297109.11 | ||
SAP30L | NM_001131062.2 | c.*1518C>T | 3_prime_UTR_variant | 3/3 | |||
SAP30L | NM_001131063.2 | c.*1518C>T | 3_prime_UTR_variant | 3/3 | |||
SAP30L | NR_024084.2 | n.2722C>T | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAP30L | ENST00000297109.11 | c.*1518C>T | 3_prime_UTR_variant | 4/4 | 1 | NM_024632.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0197 AC: 2997AN: 152126Hom.: 43 Cov.: 33
GnomAD3 genomes
?
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2997
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 16Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 12
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GnomAD4 genome ? AF: 0.0197 AC: 2993AN: 152244Hom.: 43 Cov.: 33 AF XY: 0.0194 AC XY: 1442AN XY: 74430
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?
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2993
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3478
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