chr3-151880711-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033050.6(SUCNR1):c.168C>A(p.Asn56Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033050.6 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SUCNR1 | NM_033050.6 | c.168C>A | p.Asn56Lys | missense_variant | Exon 3 of 3 | ENST00000362032.6 | NP_149039.2 | |
AADACL2-AS1 | NR_110202.1 | n.319+47146G>T | intron_variant | Intron 1 of 3 | ||||
AADACL2-AS1 | NR_110203.1 | n.319+47146G>T | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUCNR1 | ENST00000362032.6 | c.168C>A | p.Asn56Lys | missense_variant | Exon 3 of 3 | 1 | NM_033050.6 | ENSP00000355156.4 | ||
AADACL2-AS1 | ENST00000475855.1 | n.319+47146G>T | intron_variant | Intron 1 of 3 | 5 | |||||
AADACL2-AS1 | ENST00000483843.6 | n.439+36904G>T | intron_variant | Intron 2 of 4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461800Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727214
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.168C>A (p.N56K) alteration is located in exon 3 (coding exon 2) of the SUCNR1 gene. This alteration results from a C to A substitution at nucleotide position 168, causing the asparagine (N) at amino acid position 56 to be replaced by a lysine (K). 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.