17-68990854-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080283.4(ABCA9):c.3820G>A(p.Val1274Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,872 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. V1274V) has been classified as Likely benign.
Frequency
Consequence
NM_080283.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCA9 | NM_080283.4 | c.3820G>A | p.Val1274Met | missense_variant | 29/39 | ENST00000340001.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCA9 | ENST00000340001.9 | c.3820G>A | p.Val1274Met | missense_variant | 29/39 | 1 | NM_080283.4 | P1 | |
ABCA9-AS1 | ENST00000630625.1 | n.378-21129C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
ABCA9 | ENST00000453985.6 | c.3706G>A | p.Val1236Met | missense_variant | 28/38 | 5 | |||
ABCA9 | ENST00000460872.1 | n.612G>A | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250442Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135370
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460872Hom.: 1 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726744
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.3820G>A (p.V1274M) alteration is located in exon 29 (coding exon 28) of the ABCA9 gene. This alteration results from a G to A substitution at nucleotide position 3820, causing the valine (V) at amino acid position 1274 to be replaced by a methionine (M). 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