2-39120402-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_005633.4(SOS1):c.21C>T(p.Pro7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000005 in 1,598,578 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P7P) has been classified as Likely benign.
Frequency
Consequence
NM_005633.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOS1 | NM_005633.4 | c.21C>T | p.Pro7= | synonymous_variant | 1/23 | ENST00000402219.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOS1 | ENST00000402219.8 | c.21C>T | p.Pro7= | synonymous_variant | 1/23 | 1 | NM_005633.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152112Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00000437 AC: 1AN: 229012Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 126136
GnomAD4 exome AF: 0.00000346 AC: 5AN: 1446466Hom.: 0 Cov.: 31 AF XY: 0.00000278 AC XY: 2AN XY: 719622
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152112Hom.: 1 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74296
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 12, 2013 | Pro7Pro in exon 1 of SOS1: This variant is not expected to have clinical signifi cance because it does not alter an amino acid residue and is not located within the splice consensus sequence. - |
Noonan syndrome 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | SOS1: BP4, BP7 - |
Fibromatosis, gingival, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | - | - - |
RASopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at