2-18563896-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_033253.4(NT5C1B):c.1553G>A(p.Arg518Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R518W) has been classified as Uncertain significance.
Frequency
Consequence
NM_033253.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NT5C1B | ENST00000304081.9 | c.1553G>A | p.Arg518Gln | missense_variant | Exon 9 of 9 | 1 | NM_033253.4 | ENSP00000305979.4 | ||
NT5C1B-RDH14 | ENST00000532967.5 | c.1733G>A | p.Arg578Gln | missense_variant | Exon 10 of 11 | 2 | ENSP00000433415.1 | |||
NT5C1B | ENST00000406971.6 | n.*874G>A | non_coding_transcript_exon_variant | Exon 10 of 10 | 5 | ENSP00000383905.2 | ||||
NT5C1B | ENST00000406971.6 | n.*874G>A | 3_prime_UTR_variant | Exon 10 of 10 | 5 | ENSP00000383905.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251432Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135890
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461858Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 727232
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1784G>A (p.R595Q) alteration is located in exon 10 (coding exon 10) of the NT5C1B gene. This alteration results from a G to A substitution at nucleotide position 1784, causing the arginine (R) at amino acid position 595 to be replaced by a glutamine (Q). 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