chr1-24157196-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_170743.4(IFNLR1):c.1497G>A(p.Trp499Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_170743.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNLR1 | NM_170743.4 | c.1497G>A | p.Trp499Ter | stop_gained | 7/7 | ENST00000327535.6 | |
LOC124903879 | XR_007065544.1 | n.488-59C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNLR1 | ENST00000327535.6 | c.1497G>A | p.Trp499Ter | stop_gained | 7/7 | 1 | NM_170743.4 | P1 | |
IFNLR1 | ENST00000374421.7 | c.1410G>A | p.Trp470Ter | stop_gained | 7/7 | 1 | |||
IFNLR1 | ENST00000327575.6 | c.*631G>A | 3_prime_UTR_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461868Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727236
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | IFNLR1: PM2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.