1-156807305-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003975.4(SH2D2A):c.1043T>A(p.Ile348Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000628 in 1,592,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003975.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH2D2A | NM_003975.4 | c.1043T>A | p.Ile348Asn | missense_variant | 8/9 | ENST00000368199.8 | NP_003966.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH2D2A | ENST00000368199.8 | c.1043T>A | p.Ile348Asn | missense_variant | 8/9 | 1 | NM_003975.4 | ENSP00000357182 | P2 | |
SH2D2A | ENST00000392306.2 | c.1073T>A | p.Ile358Asn | missense_variant | 8/9 | 1 | ENSP00000376123 | |||
SH2D2A | ENST00000368198.7 | c.989T>A | p.Ile330Asn | missense_variant | 8/9 | 1 | ENSP00000357181 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000347 AC: 5AN: 1440216Hom.: 0 Cov.: 33 AF XY: 0.00000140 AC XY: 1AN XY: 715342
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 15, 2024 | The c.1073T>A (p.I358N) alteration is located in exon 8 (coding exon 8) of the SH2D2A gene. This alteration results from a T to A substitution at nucleotide position 1073, causing the isoleucine (I) at amino acid position 358 to be replaced by an asparagine (N). 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