9-89178067-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_016848.6(SHC3):c.394G>A(p.Glu132Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,206,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016848.6 missense
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 |
---|---|---|---|---|---|---|---|
SHC3 | NM_016848.6 | c.394G>A | p.Glu132Lys | missense_variant | 1/12 | ENST00000375835.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHC3 | ENST00000375835.9 | c.394G>A | p.Glu132Lys | missense_variant | 1/12 | 1 | NM_016848.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000662 AC: 1AN: 151130Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000171 AC: 18AN: 1055574Hom.: 0 Cov.: 29 AF XY: 0.0000160 AC XY: 8AN XY: 499170
GnomAD4 genome ? AF: 0.00000662 AC: 1AN: 151130Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 73816
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2022 | The c.394G>A (p.E132K) alteration is located in exon 1 (coding exon 1) of the SHC3 gene. This alteration results from a G to A substitution at nucleotide position 394, causing the glutamic acid (E) at amino acid position 132 to be replaced by a lysine (K). 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