chr2-208239072-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005896.4(IDH1):c.1153A>G(p.Asn385Asp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000342 in 1,461,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. N385N) has been classified as Likely benign.
Frequency
Consequence
NM_005896.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH1 | NM_005896.4 | c.1153A>G | p.Asn385Asp | missense_variant, splice_region_variant | 9/10 | ENST00000345146.7 | |
IDH1 | NM_001282386.1 | c.1153A>G | p.Asn385Asp | missense_variant, splice_region_variant | 9/10 | ||
IDH1 | NM_001282387.1 | c.1153A>G | p.Asn385Asp | missense_variant, splice_region_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH1 | ENST00000345146.7 | c.1153A>G | p.Asn385Asp | missense_variant, splice_region_variant | 9/10 | 1 | NM_005896.4 | P1 | |
IDH1 | ENST00000415913.5 | c.1153A>G | p.Asn385Asp | missense_variant, splice_region_variant | 9/10 | 1 | P1 | ||
IDH1 | ENST00000446179.5 | c.1153A>G | p.Asn385Asp | missense_variant, splice_region_variant | 9/10 | 1 | P1 | ||
IDH1 | ENST00000484575.1 | n.615A>G | splice_region_variant, non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251090Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135728
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461456Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727038
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2023 | The p.N385D variant (also known as c.1153A>G), located in coding exon 7 of the IDH1 gene, results from an A to G substitution at nucleotide position 1153. The asparagine at codon 385 is replaced by aspartic acid, an amino acid with highly similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at