rs112783338
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_005631.5(SMO):c.2227C>A(p.Pro743Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 1,614,188 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Consequence
NM_005631.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMO | NM_005631.5 | c.2227C>A | p.Pro743Thr | missense_variant | 12/12 | ENST00000249373.8 | |
SMO | XM_047420759.1 | c.1837C>A | p.Pro613Thr | missense_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMO | ENST00000249373.8 | c.2227C>A | p.Pro743Thr | missense_variant | 12/12 | 1 | NM_005631.5 | P1 | |
ENST00000466717.1 | n.129+1103G>T | intron_variant, non_coding_transcript_variant | 3 | ||||||
SMO | ENST00000655644.1 | c.*1982C>A | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 |
Frequencies
GnomAD3 genomes ? AF: 0.000433 AC: 66AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 250950Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135802
GnomAD4 exome AF: 0.0000917 AC: 134AN: 1461820Hom.: 1 Cov.: 32 AF XY: 0.0000880 AC XY: 64AN XY: 727210
GnomAD4 genome ? AF: 0.000459 AC: 70AN: 152368Hom.: 0 Cov.: 32 AF XY: 0.000564 AC XY: 42AN XY: 74514
ClinVar
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at