rs914754937
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001159702.3(FHL1):c.889-9T>C 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 0.000174 in 1,170,211 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 72 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001159702.3 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FHL1 | NM_001159699.2 | c.737-9T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000370683.6 | |||
FHL1 | NM_001159702.3 | c.889-9T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000394155.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FHL1 | ENST00000370683.6 | c.737-9T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001159699.2 | P1 | |||
FHL1 | ENST00000394155.8 | c.889-9T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001159702.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000192 AC: 21AN: 109163Hom.: 0 Cov.: 21 AF XY: 0.000221 AC XY: 7AN XY: 31681
GnomAD3 exomes AF: 0.000166 AC: 28AN: 168269Hom.: 0 AF XY: 0.000223 AC XY: 13AN XY: 58243
GnomAD4 exome AF: 0.000172 AC: 183AN: 1061004Hom.: 0 Cov.: 30 AF XY: 0.000189 AC XY: 65AN XY: 344356
GnomAD4 genome ? AF: 0.000192 AC: 21AN: 109207Hom.: 0 Cov.: 21 AF XY: 0.000221 AC XY: 7AN XY: 31737
ClinVar
Submissions by phenotype
X-linked myopathy with postural muscle atrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 28, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at