15-48857734-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_203349.4(SHC4):c.1028A>C(p.Lys343Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 1,606,660 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.1028A>C | p.Lys343Thr | missense_variant | Exon 7 of 12 | ENST00000332408.9 | NP_976224.3 | |
SHC4 | XM_005254375.4 | c.479A>C | p.Lys160Thr | missense_variant | Exon 7 of 12 | XP_005254432.1 | ||
SHC4 | XM_047432492.1 | c.170A>C | p.Lys57Thr | missense_variant | Exon 4 of 9 | XP_047288448.1 | ||
SHC4 | XM_047432493.1 | c.170A>C | p.Lys57Thr | missense_variant | Exon 5 of 10 | XP_047288449.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249232Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134798
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1454380Hom.: 0 Cov.: 30 AF XY: 0.00000276 AC XY: 2AN XY: 723374
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1028A>C (p.K343T) alteration is located in exon 7 (coding exon 7) of the SHC4 gene. This alteration results from a A to C substitution at nucleotide position 1028, causing the lysine (K) at amino acid position 343 to be replaced by a threonine (T). 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