chr20-62260044-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144498.4(OSBPL2):āc.101T>Cā(p.Ile34Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,342 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 (ā ).
Frequency
Consequence
NM_144498.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OSBPL2 | NM_144498.4 | c.101T>C | p.Ile34Thr | missense_variant | 3/14 | ENST00000313733.9 | NP_653081.1 | |
OSBPL2 | NM_014835.5 | c.65T>C | p.Ile22Thr | missense_variant | 3/14 | NP_055650.1 | ||
OSBPL2 | NM_001363878.2 | c.-266T>C | 5_prime_UTR_variant | 3/15 | NP_001350807.1 | |||
OSBPL2 | NM_001278649.3 | c.-184-3572T>C | intron_variant | NP_001265578.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OSBPL2 | ENST00000313733.9 | c.101T>C | p.Ile34Thr | missense_variant | 3/14 | 1 | NM_144498.4 | ENSP00000316649 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251448Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135906
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461210Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726952
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.101T>C (p.I34T) alteration is located in exon 3 (coding exon 2) of the OSBPL2 gene. This alteration results from a T to C substitution at nucleotide position 101, causing the isoleucine (I) at amino acid position 34 to be replaced by a threonine (T). 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