rs116702241
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001351169.2(NT5C2):c.1662A>T(p.Glu554Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 1,609,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. E554E) has been classified as Likely benign.
Frequency
Consequence
NM_001351169.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5C2 | NM_001351169.2 | c.1662A>T | p.Glu554Asp | missense_variant | 19/19 | ENST00000404739.8 | |
CNNM2 | NM_017649.5 | c.*12516T>A | 3_prime_UTR_variant | 8/8 | ENST00000369878.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5C2 | ENST00000404739.8 | c.1662A>T | p.Glu554Asp | missense_variant | 19/19 | 1 | NM_001351169.2 | P1 | |
CNNM2 | ENST00000369878.9 | c.*12516T>A | 3_prime_UTR_variant | 8/8 | 1 | NM_017649.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246642Hom.: 0 AF XY: 0.0000375 AC XY: 5AN XY: 133186
GnomAD4 exome AF: 0.00000617 AC: 9AN: 1457542Hom.: 0 Cov.: 30 AF XY: 0.00000828 AC XY: 6AN XY: 724848
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74420
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at