rs1431337923
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate
The ENST00000644641.2(SLC18A2):c.835-2_835-1delAG variant causes a splice acceptor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,776 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
ENST00000644641.2 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC18A2 | ENST00000644641.2 | c.835-2_835-1delAG | splice_acceptor_variant, intron_variant | Intron 8 of 15 | NM_003054.6 | ENSP00000496339.1 | ||||
SLC18A2 | ENST00000497497.1 | n.1251-2_1251-1delAG | splice_acceptor_variant, intron_variant | Intron 7 of 14 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251324Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135838
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461776Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 727196
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
Lines of evidence used in support of classification: LIKELY POSITIVE: Relevant Alteration(s) Detected -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at