9-33922874-A-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001370062.2(UBAP2):c.3077T>G(p.Phe1026Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000995 in 1,597,622 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370062.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBAP2 | NM_001370062.2 | c.3077T>G | p.Phe1026Cys | missense_variant | Exon 28 of 29 | ENST00000379238.7 | NP_001356991.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000177 AC: 43AN: 242786Hom.: 1 AF XY: 0.000153 AC XY: 20AN XY: 131100
GnomAD4 exome AF: 0.000103 AC: 149AN: 1445344Hom.: 2 Cov.: 33 AF XY: 0.000110 AC XY: 79AN XY: 716696
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3077T>G (p.F1026C) alteration is located in exon 28 (coding exon 27) of the UBAP2 gene. This alteration results from a T to G substitution at nucleotide position 3077, causing the phenylalanine (F) at amino acid position 1026 to be replaced by a cysteine (C). 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