1-24157795-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.898A>Gā(p.Arg300Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,614,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 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.898A>G | p.Arg300Gly | missense_variant | 7/7 | ENST00000327535.6 | |
LOC124903879 | XR_007065544.1 | n.1028T>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNLR1 | ENST00000327535.6 | c.898A>G | p.Arg300Gly | missense_variant | 7/7 | 1 | NM_170743.4 | P1 | |
IFNLR1 | ENST00000374421.7 | c.811A>G | p.Arg271Gly | missense_variant | 7/7 | 1 | |||
IFNLR1 | ENST00000327575.6 | c.*32A>G | 3_prime_UTR_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251342Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135830
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461830Hom.: 0 Cov.: 33 AF XY: 0.0000413 AC XY: 30AN XY: 727224
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.898A>G (p.R300G) 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 898, causing the arginine (R) at amino acid position 300 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