chr1-24157159-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
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNLR1 | NM_170743.4 | c.1534C>T | p.Arg512Trp | missense_variant | 7/7 | ENST00000327535.6 | |
LOC124903879 | XR_007065544.1 | n.488-96G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNLR1 | ENST00000327535.6 | c.1534C>T | p.Arg512Trp | missense_variant | 7/7 | 1 | NM_170743.4 | P1 | |
IFNLR1 | ENST00000374421.7 | c.1447C>T | p.Arg483Trp | missense_variant | 7/7 | 1 | |||
IFNLR1 | ENST00000327575.6 | c.*668C>T | 3_prime_UTR_variant | 6/6 | 1 |
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
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at