20-1635269-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018556.4(SIRPG):c.1079C>G(p.Pro360Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,448,310 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018556.4 missense, splice_region
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.1079C>G | p.Pro360Arg | missense_variant, splice_region_variant | 4/6 | ENST00000303415.7 | |
SIRPG-AS1 | NR_110090.1 | n.213+1549G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIRPG | ENST00000303415.7 | c.1079C>G | p.Pro360Arg | missense_variant, splice_region_variant | 4/6 | 1 | NM_018556.4 | P2 | |
SIRPG-AS1 | ENST00000456177.5 | n.213+1549G>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245696Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133082
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1448310Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 718268
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 04, 2023 | The c.1079C>G (p.P360R) alteration is located in exon 4 (coding exon 4) of the SIRPG gene. This alteration results from a C to G substitution at nucleotide position 1079, causing the proline (P) at amino acid position 360 to be replaced by an arginine (R). 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