rs2071397
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000169.3(GLA):c.640-16A>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000748 in 1,069,251 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_000169.3 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLA | NM_000169.3 | c.640-16A>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000218516.4 | |||
RPL36A-HNRNPH2 | NM_001199973.2 | c.300+3505T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLA | ENST00000218516.4 | c.640-16A>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000169.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183214Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67718
GnomAD4 exome AF: 0.00000748 AC: 8AN: 1069251Hom.: 0 Cov.: 28 AF XY: 0.00000886 AC XY: 3AN XY: 338497
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
Fabry disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at