NM_030777.4:c.1547+18T>G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_030777.4(SLC2A10):c.1547+18T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 1,611,072 control chromosomes in the GnomAD database, including 141,855 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_030777.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.376 AC: 56918AN: 151560Hom.: 11559 Cov.: 31
GnomAD3 exomes AF: 0.418 AC: 104878AN: 250922Hom.: 22616 AF XY: 0.417 AC XY: 56542AN XY: 135740
GnomAD4 exome AF: 0.418 AC: 610606AN: 1459404Hom.: 130285 Cov.: 38 AF XY: 0.416 AC XY: 302134AN XY: 726134
GnomAD4 genome AF: 0.376 AC: 56954AN: 151668Hom.: 11570 Cov.: 31 AF XY: 0.380 AC XY: 28180AN XY: 74064
ClinVar
Submissions by phenotype
not specified Benign:5
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Variant summary: SLC2A10 c.1547+18T>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.42 in 250922 control chromosomes, predominantly at a frequency of 0.61 within the East Asian subpopulation in the gnomAD database, including 3377 homozygotes. Therefore, suggesting the variant is the major allele found in population(s) of East Asian origin. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign. -
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Arterial tortuosity syndrome Benign:2
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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