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GeneBe

rs12979860

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong

The ENST00000634967(IFNL4):c.152-152G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 152076 control chromosomes in the gnomAD Genomes 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: 33)

Consequence

IFNL4
ENST00000634967 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.79

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, gnomad allele frequency = 0.0000132 (2/152076) while in subpopulation AFR AF= 0.0000483 (2/41414). AF 95% confidence interval is 0.000008. There are 0 homozygotes in gnomad. There are 1 alleles in male gnomad subpopulation. Median coverage is 33. This position pass quality control queck.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IFNL4NR_074079.1 linkuse as main transcriptn.429-152G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IFNL4ENST00000606380.2 linkuse as main transcriptc.152-152G>C intron_variant 1 A2
IFNL4ENST00000634680.1 linkuse as main transcriptc.151+282G>C intron_variant 1 A2
IFNL4ENST00000634967.1 linkuse as main transcriptc.152-152G>C intron_variant 1 P5

Frequencies

GnomAD3 genomes
AF:
0.0000132
AC:
2
AN:
152076
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
0.19
Dann
Benign
0.77

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: rs12979860; hg19: chr19-39738787;