chr2-85434978-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001394463.1(SH2D6):c.590-87C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000635 in 1,574,308 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 Likely benign (★).
Frequency
Consequence
NM_001394463.1 intron
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH2D6 | NM_001394463.1 | c.590-87C>T | intron_variant | Intron 19 of 23 | ENST00000469800.7 | NP_001381392.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH2D6 | ENST00000469800.7 | c.590-87C>T | intron_variant | Intron 19 of 23 | 3 | NM_001394463.1 | ENSP00000510308.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000274 AC: 5AN: 182782Hom.: 0 AF XY: 0.0000202 AC XY: 2AN XY: 99038
GnomAD4 exome AF: 0.00000492 AC: 7AN: 1422238Hom.: 0 Cov.: 45 AF XY: 0.00000426 AC XY: 3AN XY: 704016
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74276
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at