chr16-1685576-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_144570.3(JPT2):c.182C>T(p.Thr61Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000248 in 1,613,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144570.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JPT2 | ENST00000248098.8 | c.182C>T | p.Thr61Ile | missense_variant | Exon 2 of 5 | 1 | NM_144570.3 | ENSP00000248098.3 | ||
ENSG00000261732 | ENST00000454337.1 | n.*3989C>T | non_coding_transcript_exon_variant | Exon 22 of 23 | 2 | ENSP00000399780.1 | ||||
ENSG00000261732 | ENST00000454337.1 | n.*3989C>T | 3_prime_UTR_variant | Exon 22 of 23 | 2 | ENSP00000399780.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250766Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135530
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461608Hom.: 0 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 727110
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.182C>T (p.T61I) alteration is located in exon 2 (coding exon 2) of the HN1L gene. This alteration results from a C to T substitution at nucleotide position 182, causing the threonine (T) at amino acid position 61 to be replaced by an isoleucine (I). 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