X-21945025-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004595.5(SMS):c.49+4152A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 110,159 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004595.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMS | NM_004595.5 | c.49+4152A>C | intron_variant | ENST00000404933.7 | |||
SMS | NM_001258423.2 | c.49+4152A>C | intron_variant | ||||
SMS | XM_011545568.3 | c.-54+3658A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMS | ENST00000404933.7 | c.49+4152A>C | intron_variant | 1 | NM_004595.5 | P1 | |||
SMS | ENST00000379404.5 | c.49+4152A>C | intron_variant | 3 | |||||
SMS | ENST00000457085.2 | c.394+3658A>C | intron_variant | 5 | |||||
SMS | ENST00000478094.1 | n.96+4152A>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000182 AC: 2AN: 110159Hom.: 0 Cov.: 22 AF XY: 0.0000308 AC XY: 1AN XY: 32425
GnomAD4 genome AF: 0.0000182 AC: 2AN: 110159Hom.: 0 Cov.: 22 AF XY: 0.0000308 AC XY: 1AN XY: 32425
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at