chr16-1685465-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144570.3(JPT2):c.71C>T(p.Ser24Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,614,152 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 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JPT2 | ENST00000248098.8 | c.71C>T | p.Ser24Leu | missense_variant | Exon 2 of 5 | 1 | NM_144570.3 | ENSP00000248098.3 | ||
ENSG00000261732 | ENST00000454337.1 | n.*3878C>T | non_coding_transcript_exon_variant | Exon 22 of 23 | 2 | ENSP00000399780.1 | ||||
ENSG00000261732 | ENST00000454337.1 | n.*3878C>T | 3_prime_UTR_variant | Exon 22 of 23 | 2 | ENSP00000399780.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251434Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135888
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461846Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 727226
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.71C>T (p.S24L) 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 71, causing the serine (S) at amino acid position 24 to be replaced by a leucine (L). 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