16-89554524-C-A
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_003119.4(SPG7):c.2142C>A(p.Thr714Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,306 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T714T) has been classified as Likely benign.
Frequency
Consequence
NM_003119.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- hereditary spastic paraplegia 7Inheritance: AR, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Laboratory for Molecular Medicine, G2P, Orphanet, Labcorp Genetics (formerly Invitae)
- lateral sclerosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPG7 | NM_003119.4 | c.2142C>A | p.Thr714Thr | synonymous_variant | Exon 16 of 17 | ENST00000645818.2 | NP_003110.1 | |
SPG7 | NM_001363850.1 | c.2142C>A | p.Thr714Thr | synonymous_variant | Exon 16 of 18 | NP_001350779.1 | ||
SPG7 | XM_047434537.1 | c.1269C>A | p.Thr423Thr | synonymous_variant | Exon 11 of 13 | XP_047290493.1 | ||
SPG7 | XM_047434540.1 | c.828C>A | p.Thr276Thr | synonymous_variant | Exon 8 of 9 | XP_047290496.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457306Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 724982 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
Age Distribution
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at