11-34113709-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024662.3(NAT10):c.373-7C>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 0.00284 in 1,601,780 control chromosomes in the GnomAD database, including 94 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 (★★).
Frequency
Consequence
NM_024662.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAT10 | NM_024662.3 | c.373-7C>T | splice_region_variant, intron_variant | Intron 4 of 28 | ENST00000257829.8 | NP_078938.3 | ||
NAT10 | NM_001144030.2 | c.157-7C>T | splice_region_variant, intron_variant | Intron 2 of 26 | NP_001137502.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAT10 | ENST00000257829.8 | c.373-7C>T | splice_region_variant, intron_variant | Intron 4 of 28 | 1 | NM_024662.3 | ENSP00000257829.3 | |||
NAT10 | ENST00000531159.6 | c.157-7C>T | splice_region_variant, intron_variant | Intron 2 of 26 | 2 | ENSP00000433011.2 | ||||
NAT10 | ENST00000527971.5 | c.373-7C>T | splice_region_variant, intron_variant | Intron 3 of 7 | 2 | ENSP00000437324.1 | ||||
NAT10 | ENST00000529523.5 | c.373-7C>T | splice_region_variant, intron_variant | Intron 4 of 4 | 4 | ENSP00000435569.1 |
Frequencies
GnomAD3 genomes AF: 0.0151 AC: 2281AN: 150602Hom.: 46 Cov.: 31
GnomAD3 exomes AF: 0.00399 AC: 996AN: 249448Hom.: 21 AF XY: 0.00298 AC XY: 402AN XY: 134852
GnomAD4 exome AF: 0.00155 AC: 2246AN: 1451096Hom.: 46 Cov.: 34 AF XY: 0.00135 AC XY: 976AN XY: 721852
GnomAD4 genome AF: 0.0153 AC: 2298AN: 150684Hom.: 48 Cov.: 31 AF XY: 0.0149 AC XY: 1093AN XY: 73496
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at