chr10-80609469-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001388272.1(SH2D4B):c.906C>G(p.Ile302Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,461,870 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. I302T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001388272.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH2D4B | NM_001388272.1 | c.906C>G | p.Ile302Met | missense_variant | 6/8 | ENST00000646907.2 | |
SH2D4B | NM_207372.2 | c.903C>G | p.Ile301Met | missense_variant | 6/7 | ||
SH2D4B | NM_001145719.1 | c.759C>G | p.Ile253Met | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D4B | ENST00000646907.2 | c.906C>G | p.Ile302Met | missense_variant | 6/8 | NM_001388272.1 | P1 | ||
SH2D4B | ENST00000339284.6 | c.903C>G | p.Ile301Met | missense_variant | 6/7 | 2 | |||
SH2D4B | ENST00000313455.5 | c.759C>G | p.Ile253Met | missense_variant | 6/7 | 2 | |||
SH2D4B | ENST00000372150.7 | n.248C>G | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251450Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135902
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461870Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727240
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.903C>G (p.I301M) alteration is located in exon 6 (coding exon 6) of the SH2D4B gene. This alteration results from a C to G substitution at nucleotide position 903, causing the isoleucine (I) at amino acid position 301 to be replaced by a methionine (M). 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