19-17255570-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031941.4(USHBP1):c.1507G>A(p.Val503Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,612,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031941.4 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 |
---|---|---|---|---|---|---|---|
USHBP1 | NM_031941.4 | c.1507G>A | p.Val503Met | missense_variant | 10/13 | ENST00000252597.8 | |
USHBP1 | NM_001321417.2 | c.1507G>A | p.Val503Met | missense_variant | 10/13 | ||
USHBP1 | NM_001297703.2 | c.1315G>A | p.Val439Met | missense_variant | 9/12 | ||
USHBP1 | NR_135632.2 | n.1748G>A | non_coding_transcript_exon_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USHBP1 | ENST00000252597.8 | c.1507G>A | p.Val503Met | missense_variant | 10/13 | 1 | NM_031941.4 | P1 | |
USHBP1 | ENST00000431146.6 | c.1315G>A | p.Val439Met | missense_variant | 9/12 | 2 | |||
USHBP1 | ENST00000324554.9 | c.*473G>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/14 | 2 | ||||
USHBP1 | ENST00000597928.5 | c.*2627G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244736Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133498
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1460306Hom.: 0 Cov.: 33 AF XY: 0.0000358 AC XY: 26AN XY: 726358
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2022 | The c.1507G>A (p.V503M) alteration is located in exon 10 (coding exon 9) of the USHBP1 gene. This alteration results from a G to A substitution at nucleotide position 1507, causing the valine (V) at amino acid position 503 to be replaced by a methionine (M). 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