7-129189311-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBS1_Supporting
The NM_005631.5(SMO):c.160G>A(p.Val54Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000854 in 1,483,176 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_005631.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMO | NM_005631.5 | c.160G>A | p.Val54Met | missense_variant | 1/12 | ENST00000249373.8 | NP_005622.1 | |
SMO | XM_047420759.1 | c.-345G>A | 5_prime_UTR_premature_start_codon_gain_variant | 1/13 | XP_047276715.1 | |||
SMO | XM_047420759.1 | c.-345G>A | 5_prime_UTR_variant | 1/13 | XP_047276715.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMO | ENST00000249373.8 | c.160G>A | p.Val54Met | missense_variant | 1/12 | 1 | NM_005631.5 | ENSP00000249373.3 | ||
SMO | ENST00000655644.1 | n.160G>A | non_coding_transcript_exon_variant | 1/12 | ENSP00000499377.1 |
Frequencies
GnomAD3 genomes AF: 0.000618 AC: 94AN: 152036Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000546 AC: 45AN: 82464Hom.: 0 AF XY: 0.000532 AC XY: 25AN XY: 46988
GnomAD4 exome AF: 0.000882 AC: 1174AN: 1331030Hom.: 1 Cov.: 31 AF XY: 0.000885 AC XY: 580AN XY: 655670
GnomAD4 genome AF: 0.000611 AC: 93AN: 152146Hom.: 1 Cov.: 32 AF XY: 0.000471 AC XY: 35AN XY: 74388
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 27793025, 29533785, 28838384) - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | St. Jude Molecular Pathology, St. Jude Children's Research Hospital | Aug 19, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at