chr15-48857762-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_203349.4(SHC4):āc.1000A>Gā(p.Ile334Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 1,606,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I334T) has been classified 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHC4 | NM_203349.4 | c.1000A>G | p.Ile334Val | missense_variant | 7/12 | ENST00000332408.9 | |
SHC4 | XM_005254375.4 | c.451A>G | p.Ile151Val | missense_variant | 7/12 | ||
SHC4 | XM_047432492.1 | c.142A>G | p.Ile48Val | missense_variant | 4/9 | ||
SHC4 | XM_047432493.1 | c.142A>G | p.Ile48Val | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHC4 | ENST00000332408.9 | c.1000A>G | p.Ile334Val | missense_variant | 7/12 | 1 | NM_203349.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249234Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134766
GnomAD4 exome AF: 0.00000757 AC: 11AN: 1454022Hom.: 0 Cov.: 30 AF XY: 0.00000415 AC XY: 3AN XY: 723192
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 23, 2023 | The c.1000A>G (p.I334V) alteration is located in exon 7 (coding exon 7) of the SHC4 gene. This alteration results from a A to G substitution at nucleotide position 1000, causing the isoleucine (I) at amino acid position 334 to be replaced by a valine (V). 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