19-39237028-G-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The variant allele was found at a frequency of 0.0000264 in 1,136,258 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000028 ( 0 hom. )
Consequence
IFNL3P1
intragenic
intragenic
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.376
Publications
3 publications found
Genes affected
IFNL3P1 (HGNC:44483): (interferon lambda 3 pseudogene 1)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000595082.1. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| IFNL3P1 | ENST00000595082.1 | TSL:6 | n.79-72C>T | intron | N/A | ||||
| ENSG00000296032 | ENST00000735578.1 | n.116-6208G>A | intron | N/A | |||||
| ENSG00000296032 | ENST00000735579.1 | n.90-6208G>A | intron | N/A |
Frequencies
GnomAD3 genomes 0.0000132 AC: 2AN: 152050Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152050
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:
GnomAD4 exome AF: 0.0000284 AC: 28AN: 984208Hom.: 0 Cov.: 13 AF XY: 0.0000283 AC XY: 14AN XY: 495426 show subpopulations
GnomAD4 exome
AF:
AC:
28
AN:
984208
Hom.:
Cov.:
13
AF XY:
AC XY:
14
AN XY:
495426
show subpopulations
African (AFR)
AF:
AC:
0
AN:
23722
American (AMR)
AF:
AC:
0
AN:
28512
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18522
East Asian (EAS)
AF:
AC:
0
AN:
34844
South Asian (SAS)
AF:
AC:
0
AN:
61896
European-Finnish (FIN)
AF:
AC:
0
AN:
41826
Middle Eastern (MID)
AF:
AC:
0
AN:
4028
European-Non Finnish (NFE)
AF:
AC:
28
AN:
726946
Other (OTH)
AF:
AC:
0
AN:
43912
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.489
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<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 0.0000132 AC: 2AN: 152050Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74254 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152050
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
74254
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41392
American (AMR)
AF:
AC:
0
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5170
South Asian (SAS)
AF:
AC:
0
AN:
4828
European-Finnish (FIN)
AF:
AC:
0
AN:
10602
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
2
AN:
68008
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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