X-109535925-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000218004.5(NXT2):āc.43G>Cā(p.Gly15Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000475 in 1,205,160 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 212 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
ENST00000218004.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NXT2 | NM_018698.5 | c.43G>C | p.Gly15Arg | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NXT2 | ENST00000218004.5 | c.43G>C | p.Gly15Arg | missense_variant | 1/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000599 AC: 67AN: 111761Hom.: 0 Cov.: 23 AF XY: 0.000530 AC XY: 18AN XY: 33939
GnomAD3 exomes AF: 0.000454 AC: 81AN: 178600Hom.: 0 AF XY: 0.000411 AC XY: 26AN XY: 63262
GnomAD4 exome AF: 0.000463 AC: 506AN: 1093346Hom.: 0 Cov.: 26 AF XY: 0.000540 AC XY: 194AN XY: 358984
GnomAD4 genome AF: 0.000599 AC: 67AN: 111814Hom.: 0 Cov.: 23 AF XY: 0.000529 AC XY: 18AN XY: 34002
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | NXT2: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at