1-24157153-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_170743.4(IFNLR1):āc.1540T>Cā(p.Leu514=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00868 in 1,612,476 control chromosomes in the GnomAD database, including 643 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.034 ( 248 hom., cov: 32)
Exomes š: 0.0061 ( 395 hom. )
Consequence
IFNLR1
NM_170743.4 synonymous
NM_170743.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.42
Genes affected
IFNLR1 (HGNC:18584): (interferon lambda receptor 1) The protein encoded by this gene belongs to the class II cytokine receptor family. This protein forms a receptor complex with interleukine 10 receptor, beta (IL10RB). The receptor complex has been shown to interact with three closely related cytokines, including interleukin 28A (IL28A), interleukin 28B (IL28B), and interleukin 29 (IL29). The expression of all three cytokines can be induced by viral infection. The cells overexpressing this protein have been found to have enhanced responses to IL28A and IL29, but decreased response to IL28B. Three alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 1-24157153-A-G is Benign according to our data. Variant chr1-24157153-A-G is described in ClinVar as [Benign]. Clinvar id is 3056961.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.42 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNLR1 | NM_170743.4 | c.1540T>C | p.Leu514= | synonymous_variant | 7/7 | ENST00000327535.6 | |
LOC124903879 | XR_007065544.1 | n.488-102A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNLR1 | ENST00000327535.6 | c.1540T>C | p.Leu514= | synonymous_variant | 7/7 | 1 | NM_170743.4 | P1 | |
IFNLR1 | ENST00000374421.7 | c.1453T>C | p.Leu485= | synonymous_variant | 7/7 | 1 | |||
IFNLR1 | ENST00000327575.6 | c.*674T>C | 3_prime_UTR_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0335 AC: 5101AN: 152066Hom.: 247 Cov.: 32
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GnomAD3 exomes AF: 0.0137 AC: 3433AN: 250030Hom.: 144 AF XY: 0.0131 AC XY: 1774AN XY: 135120
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GnomAD4 exome AF: 0.00608 AC: 8882AN: 1460292Hom.: 395 Cov.: 33 AF XY: 0.00668 AC XY: 4852AN XY: 726454
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GnomAD4 genome AF: 0.0336 AC: 5115AN: 152184Hom.: 248 Cov.: 32 AF XY: 0.0334 AC XY: 2488AN XY: 74416
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
IFNLR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 15, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at