3-39184075-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_194293.4(XIRP1):c.5371G>A(p.Glu1791Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,608,842 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_194293.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XIRP1 | NM_194293.4 | c.5371G>A | p.Glu1791Lys | missense_variant | 2/2 | ENST00000340369.4 | NP_919269.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XIRP1 | ENST00000340369.4 | c.5371G>A | p.Glu1791Lys | missense_variant | 2/2 | 1 | NM_194293.4 | ENSP00000343140.3 | ||
XIRP1 | ENST00000421646.1 | c.1420G>A | p.Glu474Lys | missense_variant | 2/2 | 1 | ENSP00000391645.1 | |||
XIRP1 | ENST00000396251 | c.*1578G>A | 3_prime_UTR_variant | 3/3 | 1 | ENSP00000379550.1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000109 AC: 27AN: 248172Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 133936
GnomAD4 exome AF: 0.000106 AC: 154AN: 1456638Hom.: 0 Cov.: 29 AF XY: 0.000108 AC XY: 78AN XY: 723712
GnomAD4 genome AF: 0.000118 AC: 18AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2024 | The c.5371G>A (p.E1791K) alteration is located in exon 2 (coding exon 1) of the XIRP1 gene. This alteration results from a G to A substitution at nucleotide position 5371, causing the glutamic acid (E) at amino acid position 1791 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