chr1-159951686-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033438.4(SLAMF9):c.845C>A(p.Ala282Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,614,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033438.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLAMF9 | NM_033438.4 | c.845C>A | p.Ala282Glu | missense_variant | 4/4 | ENST00000368093.4 | |
LOC124904438 | XR_007066684.1 | n.380-1891G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLAMF9 | ENST00000368093.4 | c.845C>A | p.Ala282Glu | missense_variant | 4/4 | 1 | NM_033438.4 | P1 | |
SLAMF9 | ENST00000368092.7 | c.572C>A | p.Ala191Glu | missense_variant | 3/3 | 1 | |||
SLAMF9 | ENST00000466773.5 | n.502C>A | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
SLAMF9 | ENST00000489098.1 | n.483C>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 727214
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2023 | The c.845C>A (p.A282E) alteration is located in exon 4 (coding exon 4) of the SLAMF9 gene. This alteration results from a C to A substitution at nucleotide position 845, causing the alanine (A) at amino acid position 282 to be replaced by a glutamic acid (E). 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