chr13-21140586-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005870.5(SAP18):c.34C>A(p.Arg12Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,605,602 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005870.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAP18 | NM_005870.5 | c.34C>A | p.Arg12Ser | missense_variant | 1/4 | ENST00000382533.9 | |
SAP18 | NM_001366643.2 | c.-172C>A | 5_prime_UTR_variant | 1/5 | |||
SAP18 | NR_172492.1 | n.468C>A | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAP18 | ENST00000382533.9 | c.34C>A | p.Arg12Ser | missense_variant | 1/4 | 1 | NM_005870.5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000678 AC: 16AN: 235834Hom.: 0 AF XY: 0.0000548 AC XY: 7AN XY: 127840
GnomAD4 exome AF: 0.0000261 AC: 38AN: 1453400Hom.: 0 Cov.: 31 AF XY: 0.0000305 AC XY: 22AN XY: 722388
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2021 | The c.34C>A (p.R12S) alteration is located in exon 1 (coding exon 1) of the SAP18 gene. This alteration results from a C to A substitution at nucleotide position 34, causing the arginine (R) at amino acid position 12 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at