1-154486012-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001010846.3(SHE):c.1232C>T(p.Pro411Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,613,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001010846.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.1232C>T | p.Pro411Leu | missense_variant | 5/6 | ENST00000304760.3 | |
SHE | XM_011509163.4 | c.1232C>T | p.Pro411Leu | missense_variant | 5/7 | ||
SHE | XM_005244891.6 | c.1232C>T | p.Pro411Leu | missense_variant | 5/6 | ||
SHE | NR_135169.2 | n.1613C>T | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHE | ENST00000304760.3 | c.1232C>T | p.Pro411Leu | missense_variant | 5/6 | 1 | NM_001010846.3 | P1 | |
SHE | ENST00000555188.5 | c.326C>T | p.Pro109Leu | missense_variant | 3/3 | 1 | |||
SHE | ENST00000486773.1 | c.35C>T | p.Pro12Leu | missense_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251482Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135918
GnomAD4 exome AF: 0.000131 AC: 191AN: 1461814Hom.: 0 Cov.: 31 AF XY: 0.000120 AC XY: 87AN XY: 727198
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.1232C>T (p.P411L) alteration is located in exon 5 (coding exon 5) of the SHE gene. This alteration results from a C to T substitution at nucleotide position 1232, causing the proline (P) at amino acid position 411 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