3-67375866-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_003848.4(SUCLG2):c.1184-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,611,836 control chromosomes in the GnomAD database, including 149 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 Benign (no stars).
Frequency
Consequence
NM_003848.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SUCLG2 | NM_003848.4 | c.1184-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000307227.10 | NP_003839.2 | |||
SUCLG2 | XM_017007420.3 | c.*596C>T | 3_prime_UTR_variant | 11/11 | XP_016862909.1 | |||
SUCLG2 | NM_001177599.2 | c.1184-15098C>T | intron_variant | NP_001171070.1 | ||||
SUCLG2 | XM_047449140.1 | c.1040-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | XP_047305096.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUCLG2 | ENST00000307227.10 | c.1184-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003848.4 | ENSP00000307432 | P1 | |||
SUCLG2 | ENST00000460567.5 | c.456-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000417260 | |||||
SUCLG2 | ENST00000493112.5 | c.1184-15098C>T | intron_variant | 1 | ENSP00000419325 |
Frequencies
GnomAD3 genomes AF: 0.00888 AC: 1352AN: 152190Hom.: 10 Cov.: 33
GnomAD3 exomes AF: 0.0104 AC: 2550AN: 245600Hom.: 24 AF XY: 0.0116 AC XY: 1545AN XY: 133060
GnomAD4 exome AF: 0.0105 AC: 15304AN: 1459528Hom.: 139 Cov.: 36 AF XY: 0.0110 AC XY: 7951AN XY: 725754
GnomAD4 genome AF: 0.00889 AC: 1354AN: 152308Hom.: 10 Cov.: 33 AF XY: 0.00897 AC XY: 668AN XY: 74478
ClinVar
Submissions by phenotype
SUCLG2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 12, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at