rs142264016
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP7BS2
The ENST00000404933.7(SMS):āc.330A>Gā(p.Arg110=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000737 in 1,207,732 control chromosomes in the GnomAD database, including 1 homozygotes. There are 24 hemizygotes in GnomAD. 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 Uncertain significance (ā ).
Frequency
Consequence
ENST00000404933.7 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMS | NM_004595.5 | c.330A>G | p.Arg110= | splice_region_variant, synonymous_variant | 5/11 | ENST00000404933.7 | NP_004586.2 | |
SMS | NM_001258423.2 | c.171A>G | p.Arg57= | splice_region_variant, synonymous_variant | 3/9 | NP_001245352.1 | ||
SMS | XM_005274582.3 | c.228A>G | p.Arg76= | splice_region_variant, synonymous_variant | 5/11 | XP_005274639.1 | ||
SMS | XM_011545568.3 | c.228A>G | p.Arg76= | splice_region_variant, synonymous_variant | 5/11 | XP_011543870.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMS | ENST00000404933.7 | c.330A>G | p.Arg110= | splice_region_variant, synonymous_variant | 5/11 | 1 | NM_004595.5 | ENSP00000385746 | P1 | |
SMS | ENST00000457085.2 | c.675A>G | p.Arg225= | splice_region_variant, synonymous_variant | 5/6 | 5 | ENSP00000407366 | |||
SMS | ENST00000379404.5 | c.171A>G | p.Arg57= | splice_region_variant, synonymous_variant | 3/9 | 3 | ENSP00000368714 | |||
SMS | ENST00000478094.1 | n.283A>G | splice_region_variant, non_coding_transcript_exon_variant | 4/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000428 AC: 48AN: 112126Hom.: 0 Cov.: 23 AF XY: 0.000438 AC XY: 15AN XY: 34284
GnomAD3 exomes AF: 0.000131 AC: 24AN: 182851Hom.: 1 AF XY: 0.0000592 AC XY: 4AN XY: 67559
GnomAD4 exome AF: 0.0000374 AC: 41AN: 1095555Hom.: 1 Cov.: 29 AF XY: 0.0000249 AC XY: 9AN XY: 361101
GnomAD4 genome AF: 0.000428 AC: 48AN: 112177Hom.: 0 Cov.: 23 AF XY: 0.000437 AC XY: 15AN XY: 34345
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 08, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at