chr2-18584219-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_033253.4(NT5C1B):c.760T>A(p.Ser254Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S254F) has been classified as Uncertain significance.
Frequency
Consequence
NM_033253.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5C1B | NM_033253.4 | c.760T>A | p.Ser254Thr | missense_variant | 5/9 | ENST00000304081.9 | |
NT5C1B-RDH14 | NM_001199103.2 | c.766T>A | p.Ser256Thr | missense_variant | 5/9 | ||
LOC105373456 | XR_007086234.1 | n.722+20193A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5C1B | ENST00000304081.9 | c.760T>A | p.Ser254Thr | missense_variant | 5/9 | 1 | NM_033253.4 | P2 | |
NT5C1B | ENST00000359846.6 | c.940T>A | p.Ser314Thr | missense_variant | 6/10 | 1 | A2 | ||
NT5C1B | ENST00000490687.1 | n.1293T>A | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
NT5C1B | ENST00000406971.6 | c.*81T>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/10 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 27, 2022 | The c.991T>A (p.S331T) alteration is located in exon 6 (coding exon 6) of the NT5C1B gene. This alteration results from a T to A substitution at nucleotide position 991, causing the serine (S) at amino acid position 331 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.