chr19-17250280-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031941.4(USHBP1):āc.2057T>Cā(p.Leu686Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L686Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_031941.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USHBP1 | NM_031941.4 | c.2057T>C | p.Leu686Pro | missense_variant | 13/13 | ENST00000252597.8 | |
USHBP1 | NM_001321417.2 | c.2057T>C | p.Leu686Pro | missense_variant | 13/13 | ||
USHBP1 | NM_001297703.2 | c.1865T>C | p.Leu622Pro | missense_variant | 12/12 | ||
USHBP1 | NR_135632.2 | n.2298T>C | non_coding_transcript_exon_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USHBP1 | ENST00000252597.8 | c.2057T>C | p.Leu686Pro | missense_variant | 13/13 | 1 | NM_031941.4 | P1 | |
USHBP1 | ENST00000431146.6 | c.1865T>C | p.Leu622Pro | missense_variant | 12/12 | 2 | |||
USHBP1 | ENST00000324554.9 | c.*1023T>C | 3_prime_UTR_variant, NMD_transcript_variant | 14/14 | 2 | ||||
USHBP1 | ENST00000597928.5 | c.*3177T>C | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249864Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135418
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461296Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726946
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.2057T>C (p.L686P) alteration is located in exon 13 (coding exon 12) of the USHBP1 gene. This alteration results from a T to C substitution at nucleotide position 2057, causing the leucine (L) at amino acid position 686 to be replaced by a proline (P). 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