rs368428875
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001159699.2(FHL1):c.737-3delC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000656 in 1,162,380 control chromosomes in the GnomAD database, including 1 homozygotes. There are 168 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001159699.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FHL1 | NM_001159702.3 | c.889-3delC | splice_region_variant, intron_variant | Intron 7 of 7 | ENST00000394155.8 | NP_001153174.1 | ||
FHL1 | NM_001159699.2 | c.737-3delC | splice_region_variant, intron_variant | Intron 5 of 5 | ENST00000370683.6 | NP_001153171.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FHL1 | ENST00000394155.8 | c.889-8delC | splice_region_variant, intron_variant | Intron 7 of 7 | 5 | NM_001159702.3 | ENSP00000377710.2 | |||
FHL1 | ENST00000370683.6 | c.737-8delC | splice_region_variant, intron_variant | Intron 5 of 5 | 1 | NM_001159699.2 | ENSP00000359717.1 |
Frequencies
GnomAD3 genomes AF: 0.00147 AC: 160AN: 109147Hom.: 0 Cov.: 20 AF XY: 0.00101 AC XY: 32AN XY: 31665
GnomAD3 exomes AF: 0.00130 AC: 219AN: 168269Hom.: 1 AF XY: 0.000498 AC XY: 29AN XY: 58243
GnomAD4 exome AF: 0.000572 AC: 602AN: 1053189Hom.: 1 Cov.: 32 AF XY: 0.000398 AC XY: 135AN XY: 339267
GnomAD4 genome AF: 0.00147 AC: 161AN: 109191Hom.: 0 Cov.: 20 AF XY: 0.00104 AC XY: 33AN XY: 31721
ClinVar
Submissions by phenotype
not specified Benign:4
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not provided Benign:3
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X-linked myopathy with postural muscle atrophy Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at