15-44620410-GA-GAA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_025137.4(SPG11):c.2621-8dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000722 in 1,582,566 control chromosomes in the GnomAD database, including 7 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_025137.4 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 |
---|---|---|---|---|---|---|---|---|
SPG11 | NM_025137.4 | c.2621-8dupT | splice_region_variant, intron_variant | Intron 14 of 39 | ENST00000261866.12 | NP_079413.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00359 AC: 543AN: 151274Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00110 AC: 259AN: 234770Hom.: 2 AF XY: 0.000894 AC XY: 114AN XY: 127470
GnomAD4 exome AF: 0.000419 AC: 600AN: 1431178Hom.: 3 Cov.: 27 AF XY: 0.000386 AC XY: 275AN XY: 713172
GnomAD4 genome AF: 0.00358 AC: 542AN: 151388Hom.: 4 Cov.: 32 AF XY: 0.00344 AC XY: 254AN XY: 73920
ClinVar
Submissions by phenotype
not provided Benign:2
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SPG11: BP4, BS1, BS2 -
Hereditary spastic paraplegia 11 Benign:2
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SPG11-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Hereditary spastic paraplegia Benign:1
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Amyotrophic lateral sclerosis type 5 Benign:1
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Charcot-Marie-Tooth disease axonal type 2X Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at