6-107506421-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018013.4(SOBP):c.415C>T(p.Pro139Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000254 in 1,613,920 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 Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P139Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_018013.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOBP | NM_018013.4 | c.415C>T | p.Pro139Ser | missense_variant | 3/7 | ENST00000317357.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOBP | ENST00000317357.10 | c.415C>T | p.Pro139Ser | missense_variant | 3/7 | 5 | NM_018013.4 | P1 | |
SOBP | ENST00000618129.1 | c.415C>T | p.Pro139Ser | missense_variant | 3/4 | 1 | |||
SOBP | ENST00000477448.1 | n.926C>T | non_coding_transcript_exon_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 249348Hom.: 1 AF XY: 0.0000813 AC XY: 11AN XY: 135286
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461752Hom.: 1 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727174
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | The c.415C>T (p.P139S) alteration is located in exon 3 (coding exon 3) of the SOBP gene. This alteration results from a C to T substitution at nucleotide position 415, causing the proline (P) at amino acid position 139 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Intellectual disability, anterior maxillary protrusion, and strabismus Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Apr 27, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at