chr19-422282-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_012435.3(SHC2):c.1484G>A(p.Arg495Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,954 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R495W) has been classified as Uncertain significance.
Frequency
Consequence
NM_012435.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHC2 | ENST00000264554.11 | c.1484G>A | p.Arg495Gln | missense_variant | Exon 11 of 13 | 1 | NM_012435.3 | ENSP00000264554.4 | ||
SHC2 | ENST00000588376.5 | n.547G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | 1 | |||||
SHC2 | ENST00000590170.3 | n.*7G>A | non_coding_transcript_exon_variant | Exon 4 of 6 | 5 | ENSP00000465764.3 | ||||
SHC2 | ENST00000590170.3 | n.*7G>A | 3_prime_UTR_variant | Exon 4 of 6 | 5 | ENSP00000465764.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459954Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 726248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1484G>A (p.R495Q) alteration is located in exon 11 (coding exon 11) of the SHC2 gene. This alteration results from a G to A substitution at nucleotide position 1484, causing the arginine (R) at amino acid position 495 to be replaced by a glutamine (Q). 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