chr8-19334705-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022071.4(SH2D4A):āc.361T>Gā(p.Phe121Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,451,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022071.4 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 |
---|---|---|---|---|---|---|---|
SH2D4A | NM_022071.4 | c.361T>G | p.Phe121Val | missense_variant | 4/10 | ENST00000265807.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH2D4A | ENST00000265807.8 | c.361T>G | p.Phe121Val | missense_variant | 4/10 | 2 | NM_022071.4 | P1 | |
SH2D4A | ENST00000519207.5 | c.361T>G | p.Phe121Val | missense_variant | 4/10 | 1 | P1 | ||
SH2D4A | ENST00000518040.5 | c.226T>G | p.Phe76Val | missense_variant | 3/9 | 2 | |||
SH2D4A | ENST00000523736.1 | c.319T>G | p.Phe107Val | missense_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1451108Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 721480
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.361T>G (p.F121V) alteration is located in exon 4 (coding exon 3) of the SH2D4A gene. This alteration results from a T to G substitution at nucleotide position 361, causing the phenylalanine (F) at amino acid position 121 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
Publications
No publications associated with this variant yet.