16-89532455-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BS2_Supporting
The NM_003119.4(SPG7):c.1151-8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000373 in 1,613,252 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003119.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000829 AC: 205AN: 247260Hom.: 0 AF XY: 0.00101 AC XY: 136AN XY: 134960
GnomAD4 exome AF: 0.000385 AC: 562AN: 1460952Hom.: 5 Cov.: 32 AF XY: 0.000541 AC XY: 393AN XY: 726776
GnomAD4 genome AF: 0.000256 AC: 39AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26AN XY: 74466
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Dec 12, 2016 | - - |
Hereditary spastic paraplegia 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at