17-75136011-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001002032.3(JPT1):āc.537G>Cā(p.Leu179Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000249 in 1,604,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001002032.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JPT1 | NM_016185.4 | c.*91G>C | 3_prime_UTR_variant | 5/5 | ENST00000409753.8 | NP_057269.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JPT1 | ENST00000409753.8 | c.*91G>C | 3_prime_UTR_variant | 5/5 | 1 | NM_016185.4 | ENSP00000387059.3 |
Frequencies
GnomAD3 genomes AF: 0.00000662 AC: 1AN: 150976Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245926Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133502
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1453758Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 722850
GnomAD4 genome AF: 0.00000662 AC: 1AN: 150976Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73648
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | The c.537G>C (p.L179F) alteration is located in exon 4 (coding exon 4) of the HN1 gene. This alteration results from a G to C substitution at nucleotide position 537, causing the leucine (L) at amino acid position 179 to be replaced by a phenylalanine (F). 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