16-4609787-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145253.3(UBALD1):c.380C>T(p.Ala127Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000736 in 1,507,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145253.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBALD1 | NM_145253.3 | c.380C>T | p.Ala127Val | missense_variant | Exon 3 of 3 | ENST00000283474.12 | NP_660296.1 | |
UBALD1 | NM_001330467.2 | c.305C>T | p.Ala102Val | missense_variant | Exon 3 of 3 | NP_001317396.1 | ||
UBALD1 | NM_001411032.1 | c.*196C>T | 3_prime_UTR_variant | Exon 3 of 3 | NP_001397961.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151952Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000893 AC: 13AN: 145624Hom.: 0 AF XY: 0.0000881 AC XY: 7AN XY: 79424
GnomAD4 exome AF: 0.0000767 AC: 104AN: 1355660Hom.: 0 Cov.: 32 AF XY: 0.0000632 AC XY: 42AN XY: 664470
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151952Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74212
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.380C>T (p.A127V) alteration is located in exon 3 (coding exon 3) of the UBALD1 gene. This alteration results from a C to T substitution at nucleotide position 380, causing the alanine (A) at amino acid position 127 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