19-17250394-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031941.4(USHBP1):c.1943G>A(p.Arg648Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000806 in 1,613,094 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USHBP1 | NM_031941.4 | c.1943G>A | p.Arg648Gln | missense_variant | 13/13 | ENST00000252597.8 | |
USHBP1 | NM_001321417.2 | c.1943G>A | p.Arg648Gln | missense_variant | 13/13 | ||
USHBP1 | NM_001297703.2 | c.1751G>A | p.Arg584Gln | missense_variant | 12/12 | ||
USHBP1 | NR_135632.2 | n.2184G>A | non_coding_transcript_exon_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USHBP1 | ENST00000252597.8 | c.1943G>A | p.Arg648Gln | missense_variant | 13/13 | 1 | NM_031941.4 | P1 | |
USHBP1 | ENST00000431146.6 | c.1751G>A | p.Arg584Gln | missense_variant | 12/12 | 2 | |||
USHBP1 | ENST00000324554.9 | c.*909G>A | 3_prime_UTR_variant, NMD_transcript_variant | 14/14 | 2 | ||||
USHBP1 | ENST00000597928.5 | c.*3063G>A | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000283 AC: 43AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000999 AC: 25AN: 250158Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135518
GnomAD4 exome AF: 0.0000595 AC: 87AN: 1460974Hom.: 0 Cov.: 33 AF XY: 0.0000495 AC XY: 36AN XY: 726840
GnomAD4 genome ? AF: 0.000283 AC: 43AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.1943G>A (p.R648Q) alteration is located in exon 13 (coding exon 12) of the USHBP1 gene. This alteration results from a G to A substitution at nucleotide position 1943, causing the arginine (R) at amino acid position 648 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