14-69952282-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001034852.3(SMOC1):c.244G>A(p.Val82Met) variant causes a missense change. The variant allele was found at a frequency of 0.00096 in 1,614,176 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001034852.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMOC1 | NM_001034852.3 | c.244G>A | p.Val82Met | missense_variant | 2/12 | ENST00000361956.8 | NP_001030024.1 | |
SMOC1 | NM_022137.6 | c.244G>A | p.Val82Met | missense_variant | 2/12 | NP_071420.1 | ||
SMOC1 | XM_005267995.2 | c.244G>A | p.Val82Met | missense_variant | 2/12 | XP_005268052.1 | ||
SMOC1 | XM_005267996.2 | c.244G>A | p.Val82Met | missense_variant | 2/12 | XP_005268053.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMOC1 | ENST00000361956.8 | c.244G>A | p.Val82Met | missense_variant | 2/12 | 1 | NM_001034852.3 | ENSP00000355110 | A2 | |
SMOC1 | ENST00000381280.4 | c.244G>A | p.Val82Met | missense_variant | 2/12 | 1 | ENSP00000370680 | P4 | ||
SMOC1 | ENST00000553839.1 | n.146G>A | non_coding_transcript_exon_variant | 1/4 | 5 | |||||
SMOC1 | ENST00000555917.1 | n.549G>A | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00460 AC: 700AN: 152192Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00123 AC: 310AN: 251292Hom.: 3 AF XY: 0.000957 AC XY: 130AN XY: 135804
GnomAD4 exome AF: 0.000580 AC: 848AN: 1461866Hom.: 3 Cov.: 33 AF XY: 0.000505 AC XY: 367AN XY: 727240
GnomAD4 genome AF: 0.00460 AC: 701AN: 152310Hom.: 4 Cov.: 33 AF XY: 0.00448 AC XY: 334AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at