1-20722769-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001103161.2(SH2D5):c.1055G>A(p.Arg352His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000466 in 1,523,248 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_001103161.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH2D5 | ENST00000444387.7 | c.1055G>A | p.Arg352His | missense_variant | Exon 9 of 10 | 2 | NM_001103161.2 | ENSP00000406026.2 | ||
SH2D5 | ENST00000375031.5 | c.803G>A | p.Arg268His | missense_variant | Exon 8 of 9 | 2 | ENSP00000364171.1 | |||
SH2D5 | ENST00000460804.5 | n.786G>A | non_coding_transcript_exon_variant | Exon 5 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000242 AC: 4AN: 165004Hom.: 0 AF XY: 0.0000221 AC XY: 2AN XY: 90504
GnomAD4 exome AF: 0.0000467 AC: 64AN: 1371036Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 26AN XY: 674698
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1055G>A (p.R352H) alteration is located in exon 9 (coding exon 8) of the SH2D5 gene. This alteration results from a G to A substitution at nucleotide position 1055, causing the arginine (R) at amino acid position 352 to be replaced by a histidine (H). 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