19-17251613-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_031941.4(USHBP1):c.1891G>C(p.Glu631Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,842 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E631K) has been classified 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USHBP1 | NM_031941.4 | c.1891G>C | p.Glu631Gln | missense_variant | 12/13 | ENST00000252597.8 | |
USHBP1 | NM_001321417.2 | c.1891G>C | p.Glu631Gln | missense_variant | 12/13 | ||
USHBP1 | NM_001297703.2 | c.1699G>C | p.Glu567Gln | missense_variant | 11/12 | ||
USHBP1 | NR_135632.2 | n.2132G>C | non_coding_transcript_exon_variant | 13/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USHBP1 | ENST00000252597.8 | c.1891G>C | p.Glu631Gln | missense_variant | 12/13 | 1 | NM_031941.4 | P1 | |
USHBP1 | ENST00000431146.6 | c.1699G>C | p.Glu567Gln | missense_variant | 11/12 | 2 | |||
USHBP1 | ENST00000324554.9 | c.*857G>C | 3_prime_UTR_variant, NMD_transcript_variant | 13/14 | 2 | ||||
USHBP1 | ENST00000597928.5 | c.*3011G>C | 3_prime_UTR_variant, NMD_transcript_variant | 11/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152048Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251436Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135900
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461794Hom.: 1 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727192
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152048Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 16, 2023 | The c.1891G>C (p.E631Q) alteration is located in exon 12 (coding exon 11) of the USHBP1 gene. This alteration results from a G to C substitution at nucleotide position 1891, causing the glutamic acid (E) at amino acid position 631 to be replaced by a glutamine (Q). 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