15-48867845-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_203349.4(SHC4):c.919G>A(p.Val307Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000471 in 1,613,364 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_203349.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHC4 | NM_203349.4 | c.919G>A | p.Val307Ile | missense_variant | Exon 6 of 12 | ENST00000332408.9 | NP_976224.3 | |
SHC4 | XM_005254375.4 | c.370G>A | p.Val124Ile | missense_variant | Exon 6 of 12 | XP_005254432.1 | ||
SHC4 | XM_047432492.1 | c.61G>A | p.Val21Ile | missense_variant | Exon 3 of 9 | XP_047288448.1 | ||
SHC4 | XM_047432493.1 | c.61G>A | p.Val21Ile | missense_variant | Exon 4 of 10 | XP_047288449.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152100Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251124Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135764
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461264Hom.: 0 Cov.: 29 AF XY: 0.0000426 AC XY: 31AN XY: 726962
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152100Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.919G>A (p.V307I) alteration is located in exon 6 (coding exon 6) of the SHC4 gene. This alteration results from a G to A substitution at nucleotide position 919, causing the valine (V) at amino acid position 307 to be replaced by an isoleucine (I). 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