chr2-166903729-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152381.6(XIRP2):c.247A>G(p.Lys83Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152381.6 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XIRP2 | NM_152381.6 | c.247A>G | p.Lys83Glu | missense_variant | 2/11 | ENST00000409195.6 | |
XIRP2 | NM_001199143.2 | c.247A>G | p.Lys83Glu | missense_variant | 2/11 | ||
XIRP2 | NM_001079810.4 | c.247A>G | p.Lys83Glu | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XIRP2 | ENST00000409195.6 | c.247A>G | p.Lys83Glu | missense_variant | 2/11 | 5 | NM_152381.6 | ||
XIRP2 | ENST00000409728.5 | c.247A>G | p.Lys83Glu | missense_variant | 2/11 | 1 | |||
XIRP2 | ENST00000409043.5 | c.247A>G | p.Lys83Glu | missense_variant | 2/10 | 1 | |||
XIRP2 | ENST00000672716.1 | c.271A>G | p.Lys91Glu | missense_variant | 2/10 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249078Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135136
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461482Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 727042
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74416
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | The c.247A>G (p.K83E) alteration is located in exon 2 (coding exon 1) of the XIRP2 gene. This alteration results from a A to G substitution at nucleotide position 247, causing the lysine (K) at amino acid position 83 to be replaced by a glutamic acid (E). 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