1-24157768-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_170743.4(IFNLR1):āc.925A>Gā(p.Arg309Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_170743.4 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 | UniProt |
---|---|---|---|---|---|---|---|
IFNLR1 | NM_170743.4 | c.925A>G | p.Arg309Gly | missense_variant | 7/7 | ENST00000327535.6 | |
LOC124903879 | XR_007065544.1 | n.1001T>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNLR1 | ENST00000327535.6 | c.925A>G | p.Arg309Gly | missense_variant | 7/7 | 1 | NM_170743.4 | P1 | |
IFNLR1 | ENST00000374421.7 | c.838A>G | p.Arg280Gly | missense_variant | 7/7 | 1 | |||
IFNLR1 | ENST00000327575.6 | c.*59A>G | 3_prime_UTR_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251394Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135864
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461886Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 727246
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | The c.925A>G (p.R309G) alteration is located in exon 7 (coding exon 7) of the IFNLR1 gene. This alteration results from a A to G substitution at nucleotide position 925, causing the arginine (R) at amino acid position 309 to be replaced by a glycine (G). 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