chr10-80603665-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001388272.1(SH2D4B):c.730A>T(p.Ile244Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000206 in 1,457,230 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. I244V) 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH2D4B | NM_001388272.1 | c.730A>T | p.Ile244Phe | missense_variant | 5/8 | ENST00000646907.2 | |
SH2D4B | NM_207372.2 | c.730A>T | p.Ile244Phe | missense_variant | 5/7 | ||
SH2D4B | NM_001145719.1 | c.583A>T | p.Ile195Phe | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D4B | ENST00000646907.2 | c.730A>T | p.Ile244Phe | missense_variant | 5/8 | NM_001388272.1 | P1 | ||
SH2D4B | ENST00000339284.6 | c.730A>T | p.Ile244Phe | missense_variant | 5/7 | 2 | |||
SH2D4B | ENST00000313455.5 | c.583A>T | p.Ile195Phe | missense_variant | 5/7 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1457230Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 724474
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.730A>T (p.I244F) alteration is located in exon 5 (coding exon 5) of the SH2D4B gene. This alteration results from a A to T substitution at nucleotide position 730, causing the isoleucine (I) at amino acid position 244 to be replaced by a phenylalanine (F). 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
Publications
No publications associated with this variant yet.