chr19-39245279-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The 19-39245279-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 584,244 control chromosomes in the GnomAD database, including 21,237 homozygotes. 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 0.28 ( 5609 hom., cov: 22)
Exomes 𝑓: 0.26 ( 15628 hom. )

Consequence

IFNL3
ENST00000613087.5 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.49
Variant links:
Genes affected
IFNL3 (HGNC:18365): (interferon lambda 3) This gene encodes a cytokine distantly related to type I interferons and the IL-10 family. This gene, interleukin 28A (IL28A), and interleukin 29 (IL29) 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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IFNL3NM_001346937.2 linkuse as main transcript upstream_gene_variant NP_001333866.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IFNL3ENST00000613087.5 linkuse as main transcript upstream_gene_variant 1 ENSP00000481633 P4

Frequencies

GnomAD3 genomes
AF:
0.277
AC:
40163
AN:
145134
Hom.:
5605
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.281
Gnomad AMI
AF:
0.324
Gnomad AMR
AF:
0.328
Gnomad ASJ
AF:
0.374
Gnomad EAS
AF:
0.0682
Gnomad SAS
AF:
0.189
Gnomad FIN
AF:
0.210
Gnomad MID
AF:
0.331
Gnomad NFE
AF:
0.289
Gnomad OTH
AF:
0.284
GnomAD4 exome
AF:
0.258
AC:
113229
AN:
438994
Hom.:
15628
AF XY:
0.254
AC XY:
58383
AN XY:
229590
show subpopulations
Gnomad4 AFR exome
AF:
0.277
Gnomad4 AMR exome
AF:
0.353
Gnomad4 ASJ exome
AF:
0.360
Gnomad4 EAS exome
AF:
0.0793
Gnomad4 SAS exome
AF:
0.202
Gnomad4 FIN exome
AF:
0.219
Gnomad4 NFE exome
AF:
0.279
Gnomad4 OTH exome
AF:
0.267
GnomAD4 genome
AF:
0.277
AC:
40208
AN:
145250
Hom.:
5609
Cov.:
22
AF XY:
0.270
AC XY:
19086
AN XY:
70588
show subpopulations
Gnomad4 AFR
AF:
0.282
Gnomad4 AMR
AF:
0.328
Gnomad4 ASJ
AF:
0.374
Gnomad4 EAS
AF:
0.0686
Gnomad4 SAS
AF:
0.189
Gnomad4 FIN
AF:
0.210
Gnomad4 NFE
AF:
0.289
Gnomad4 OTH
AF:
0.280
Alfa
AF:
0.297
Hom.:
678
Bravo
AF:
0.296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
9.1
DANN
Benign
0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4803219; hg19: chr19-39735919; API