chr20-1635455-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018556.4(SIRPG):c.893C>T(p.Ser298Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018556.4 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 |
---|---|---|---|---|---|---|---|
SIRPG | NM_018556.4 | c.893C>T | p.Ser298Leu | missense_variant | 4/6 | ENST00000303415.7 | |
SIRPG-AS1 | NR_110090.1 | n.213+1735G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIRPG | ENST00000303415.7 | c.893C>T | p.Ser298Leu | missense_variant | 4/6 | 1 | NM_018556.4 | P2 | |
SIRPG-AS1 | ENST00000456177.5 | n.213+1735G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000282 AC: 71AN: 251492Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135922
GnomAD4 exome AF: 0.000270 AC: 394AN: 1461856Hom.: 0 Cov.: 73 AF XY: 0.000283 AC XY: 206AN XY: 727238
GnomAD4 genome AF: 0.000151 AC: 23AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.893C>T (p.S298L) alteration is located in exon 4 (coding exon 4) of the SIRPG gene. This alteration results from a C to T substitution at nucleotide position 893, causing the serine (S) at amino acid position 298 to be replaced by a leucine (L). 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