6-31764273-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001039651.2(SAPCD1):c.359C>T(p.Pro120Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,614,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001039651.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAPCD1 | NM_001039651.2 | c.359C>T | p.Pro120Leu | missense_variant | 4/5 | ENST00000415669.4 | |
MSH5-SAPCD1 | NR_037846.1 | n.3566C>T | non_coding_transcript_exon_variant | 28/29 | |||
SAPCD1-AS1 | NR_126423.1 | n.498G>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAPCD1 | ENST00000415669.4 | c.359C>T | p.Pro120Leu | missense_variant | 4/5 | 1 | NM_001039651.2 | P2 | |
SAPCD1 | ENST00000425424.4 | c.351+114C>T | intron_variant | 5 | A2 | ||||
SAPCD1 | ENST00000494299.1 | n.548C>T | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
SAPCD1-AS1 | ENST00000419679.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251464Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135914
GnomAD4 exome AF: 0.000145 AC: 212AN: 1461722Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 88AN XY: 727166
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at