rs1885482
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001034852.3(SMOC1):c.1046+7T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,612,844 control chromosomes in the GnomAD database, including 23,863 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001034852.3 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMOC1 | NM_001034852.3 | c.1046+7T>A | splice_region_variant, intron_variant | ENST00000361956.8 | |||
SMOC1 | NM_022137.6 | c.1046+7T>A | splice_region_variant, intron_variant | ||||
SMOC1 | XM_005267995.2 | c.1079+7T>A | splice_region_variant, intron_variant | ||||
SMOC1 | XM_005267996.2 | c.1079+7T>A | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMOC1 | ENST00000361956.8 | c.1046+7T>A | splice_region_variant, intron_variant | 1 | NM_001034852.3 | A2 | |||
SMOC1 | ENST00000381280.4 | c.1046+7T>A | splice_region_variant, intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.201 AC: 30567AN: 151814Hom.: 3511 Cov.: 32
GnomAD3 exomes AF: 0.153 AC: 38477AN: 251140Hom.: 3586 AF XY: 0.146 AC XY: 19801AN XY: 135736
GnomAD4 exome AF: 0.160 AC: 233640AN: 1460912Hom.: 20354 Cov.: 31 AF XY: 0.156 AC XY: 113388AN XY: 726832
GnomAD4 genome ? AF: 0.201 AC: 30591AN: 151932Hom.: 3509 Cov.: 32 AF XY: 0.198 AC XY: 14678AN XY: 74262
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 17, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at