20-1312486-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080489.5(SDCBP2):c.583A>G(p.Met195Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,614,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080489.5 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 |
---|---|---|---|---|---|---|---|
SDCBP2 | NM_080489.5 | c.583A>G | p.Met195Val | missense_variant | 7/9 | ENST00000360779.4 | |
FKBP1A-SDCBP2 | NR_037661.1 | n.861A>G | non_coding_transcript_exon_variant | 8/10 | |||
SDCBP2 | NM_001199784.2 | c.583A>G | p.Met195Val | missense_variant | 7/9 | ||
SDCBP2 | NM_015685.6 | c.328A>G | p.Met110Val | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDCBP2 | ENST00000360779.4 | c.583A>G | p.Met195Val | missense_variant | 7/9 | 1 | NM_080489.5 | P1 | |
SDCBP2 | ENST00000339987.7 | c.583A>G | p.Met195Val | missense_variant | 7/9 | 1 | P1 | ||
SDCBP2 | ENST00000381808.7 | c.328A>G | p.Met110Val | missense_variant | 3/5 | 1 | |||
SDCBP2 | ENST00000381812.5 | c.583A>G | p.Met195Val | missense_variant | 7/9 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251204Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135824
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461864Hom.: 0 Cov.: 63 AF XY: 0.00000275 AC XY: 2AN XY: 727224
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.583A>G (p.M195V) alteration is located in exon 7 (coding exon 6) of the SDCBP2 gene. This alteration results from a A to G substitution at nucleotide position 583, causing the methionine (M) at amino acid position 195 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at