19-39298008-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_172140.2(IFNL1):c.294G>A(p.Thr98Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 1,614,158 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0072 ( 4 hom., cov: 31)
Exomes 𝑓: 0.010 ( 97 hom. )
Consequence
IFNL1
NM_172140.2 synonymous
NM_172140.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -7.77
Publications
3 publications found
Genes affected
IFNL1 (HGNC:18363): (interferon lambda 1) This gene encodes a cytokine distantly related to type I interferons and the IL-10 family. This gene, interleukin 28A (IL28A), and interleukin 28B (IL28B) are three closely related cytokine genes that form a cytokine gene cluster on a chromosomal region mapped to 19q13. Expression of the cytokines encoded by the three genes can be induced by viral infection. All three cytokines have been shown to interact with a heterodimeric class II cytokine receptor that consists of interleukin 10 receptor, beta (IL10RB) and interleukin 28 receptor, alpha (IL28RA). [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant 19-39298008-G-A is Benign according to our data. Variant chr19-39298008-G-A is described in CliVar as Benign. Clinvar id is 707833.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-39298008-G-A is described in CliVar as Benign. Clinvar id is 707833.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-7.77 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFNL1 | NM_172140.2 | c.294G>A | p.Thr98Thr | synonymous_variant | Exon 3 of 5 | ENST00000333625.3 | NP_742152.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00716 AC: 1090AN: 152176Hom.: 4 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
1090
AN:
152176
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00689 AC: 1732AN: 251328 AF XY: 0.00712 show subpopulations
GnomAD2 exomes
AF:
AC:
1732
AN:
251328
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0104 AC: 15236AN: 1461866Hom.: 97 Cov.: 31 AF XY: 0.0103 AC XY: 7524AN XY: 727238 show subpopulations
GnomAD4 exome
AF:
AC:
15236
AN:
1461866
Hom.:
Cov.:
31
AF XY:
AC XY:
7524
AN XY:
727238
show subpopulations
African (AFR)
AF:
AC:
59
AN:
33480
American (AMR)
AF:
AC:
263
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
47
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
238
AN:
86258
European-Finnish (FIN)
AF:
AC:
91
AN:
53410
Middle Eastern (MID)
AF:
AC:
51
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
13882
AN:
1111996
Other (OTH)
AF:
AC:
605
AN:
60394
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.462
Heterozygous variant carriers
0
878
1755
2633
3510
4388
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
528
1056
1584
2112
2640
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.00715 AC: 1089AN: 152292Hom.: 4 Cov.: 31 AF XY: 0.00638 AC XY: 475AN XY: 74462 show subpopulations
GnomAD4 genome
AF:
AC:
1089
AN:
152292
Hom.:
Cov.:
31
AF XY:
AC XY:
475
AN XY:
74462
show subpopulations
African (AFR)
AF:
AC:
75
AN:
41568
American (AMR)
AF:
AC:
176
AN:
15308
Ashkenazi Jewish (ASJ)
AF:
AC:
14
AN:
3470
East Asian (EAS)
AF:
AC:
1
AN:
5156
South Asian (SAS)
AF:
AC:
15
AN:
4826
European-Finnish (FIN)
AF:
AC:
19
AN:
10622
Middle Eastern (MID)
AF:
AC:
3
AN:
294
European-Non Finnish (NFE)
AF:
AC:
768
AN:
68020
Other (OTH)
AF:
AC:
18
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
55
110
165
220
275
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
7
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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