9-127744911-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_170600.3(SH2D3C):c.1453A>G(p.Ser485Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 1,605,380 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_170600.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH2D3C | NM_170600.3 | c.1453A>G | p.Ser485Gly | missense_variant | 7/12 | ENST00000314830.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D3C | ENST00000314830.13 | c.1453A>G | p.Ser485Gly | missense_variant | 7/12 | 1 | NM_170600.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152094Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000813 AC: 2AN: 245902Hom.: 0 AF XY: 0.00000753 AC XY: 1AN XY: 132858
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1453286Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 721910
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152094Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.1453A>G (p.S485G) alteration is located in exon 7 (coding exon 7) of the SH2D3C gene. This alteration results from a A to G substitution at nucleotide position 1453, causing the serine (S) at amino acid position 485 to be replaced by a glycine (G). 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