rs200965114
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_000199.5(SGSH):c.507-7C>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 0.000309 in 1,610,910 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★★).
Frequency
Consequence
NM_000199.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000545 AC: 83AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000311 AC: 75AN: 241174Hom.: 0 AF XY: 0.000312 AC XY: 41AN XY: 131532
GnomAD4 exome AF: 0.000284 AC: 414AN: 1458548Hom.: 0 Cov.: 34 AF XY: 0.000272 AC XY: 197AN XY: 725176
GnomAD4 genome AF: 0.000545 AC: 83AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.000523 AC XY: 39AN XY: 74510
ClinVar
Submissions by phenotype
not specified Benign:1
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Mucopolysaccharidosis, MPS-III-A Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at