10-80609468-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001388272.1(SH2D4B):c.905T>C(p.Ile302Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000117 in 1,614,204 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I302M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001388272.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH2D4B | NM_001388272.1 | c.905T>C | p.Ile302Thr | missense_variant | 6/8 | ENST00000646907.2 | |
SH2D4B | NM_207372.2 | c.902T>C | p.Ile301Thr | missense_variant | 6/7 | ||
SH2D4B | NM_001145719.1 | c.758T>C | p.Ile253Thr | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D4B | ENST00000646907.2 | c.905T>C | p.Ile302Thr | missense_variant | 6/8 | NM_001388272.1 | P1 | ||
SH2D4B | ENST00000339284.6 | c.902T>C | p.Ile301Thr | missense_variant | 6/7 | 2 | |||
SH2D4B | ENST00000313455.5 | c.758T>C | p.Ile253Thr | missense_variant | 6/7 | 2 | |||
SH2D4B | ENST00000372150.7 | n.247T>C | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000624 AC: 95AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000139 AC: 35AN: 251452Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135908
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1461870Hom.: 0 Cov.: 32 AF XY: 0.0000550 AC XY: 40AN XY: 727244
GnomAD4 genome ? AF: 0.000624 AC: 95AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.000483 AC XY: 36AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2021 | The c.902T>C (p.I301T) alteration is located in exon 6 (coding exon 6) of the SH2D4B gene. This alteration results from a T to C substitution at nucleotide position 902, causing the isoleucine (I) at amino acid position 301 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