chr20-1319595-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080489.5(SDCBP2):c.119C>T(p.Pro40Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000701 in 1,568,220 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDCBP2 | NM_080489.5 | c.119C>T | p.Pro40Leu | missense_variant | 3/9 | ENST00000360779.4 | |
FKBP1A-SDCBP2 | NR_037661.1 | n.397C>T | non_coding_transcript_exon_variant | 4/10 | |||
SDCBP2 | NM_001199784.2 | c.119C>T | p.Pro40Leu | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDCBP2 | ENST00000360779.4 | c.119C>T | p.Pro40Leu | missense_variant | 3/9 | 1 | NM_080489.5 | P1 | |
SDCBP2 | ENST00000339987.7 | c.119C>T | p.Pro40Leu | missense_variant | 3/9 | 1 | P1 | ||
SDCBP2 | ENST00000381812.5 | c.119C>T | p.Pro40Leu | missense_variant | 3/9 | 5 | P1 | ||
SDCBP2 | ENST00000615838.1 | n.193C>T | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000706 AC: 10AN: 1415988Hom.: 0 Cov.: 31 AF XY: 0.0000114 AC XY: 8AN XY: 699640
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.119C>T (p.P40L) alteration is located in exon 3 (coding exon 2) of the SDCBP2 gene. This alteration results from a C to T substitution at nucleotide position 119, causing the proline (P) at amino acid position 40 to be replaced by a leucine (L). 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