1-154501717-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001010846.3(SHE):c.310T>C(p.Ser104Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000998 in 1,603,180 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S104A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001010846.3 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 |
---|---|---|---|---|---|---|---|
SHE | NM_001010846.3 | c.310T>C | p.Ser104Pro | missense_variant | 1/6 | ENST00000304760.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHE | ENST00000304760.3 | c.310T>C | p.Ser104Pro | missense_variant | 1/6 | 1 | NM_001010846.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151866Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000454 AC: 1AN: 220318Hom.: 0 AF XY: 0.00000821 AC XY: 1AN XY: 121862
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1451314Hom.: 0 Cov.: 35 AF XY: 0.00000970 AC XY: 7AN XY: 721770
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151866Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74190
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | The c.310T>C (p.S104P) alteration is located in exon 1 (coding exon 1) of the SHE gene. This alteration results from a T to C substitution at nucleotide position 310, causing the serine (S) at amino acid position 104 to be replaced by a proline (P). 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