1-24157159-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_170743.4(IFNLR1):c.1534C>T(p.Arg512Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,613,236 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R512Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_170743.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFNLR1 | NM_170743.4 | c.1534C>T | p.Arg512Trp | missense_variant | 7/7 | ENST00000327535.6 | NP_734464.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFNLR1 | ENST00000327535.6 | c.1534C>T | p.Arg512Trp | missense_variant | 7/7 | 1 | NM_170743.4 | ENSP00000327824.1 | ||
IFNLR1 | ENST00000374421.7 | c.1447C>T | p.Arg483Trp | missense_variant | 7/7 | 1 | ENSP00000363542.3 | |||
IFNLR1 | ENST00000327575.6 | c.*668C>T | 3_prime_UTR_variant | 6/6 | 1 | ENSP00000328994.2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250700Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135474
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461096Hom.: 0 Cov.: 33 AF XY: 0.0000399 AC XY: 29AN XY: 726828
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2024 | The c.1534C>T (p.R512W) alteration is located in exon 7 (coding exon 7) of the IFNLR1 gene. This alteration results from a C to T substitution at nucleotide position 1534, causing the arginine (R) at amino acid position 512 to be replaced by a tryptophan (W). 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