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GeneBe

rs1800896

chr1-206773552-T-C

Variant summary

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

The NM_153758.5(IL19):c.-149+2474T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 150900 control chromosomes in the gnomAD Genomes database, including 12903 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain risk allele (no stars).

Frequency

Genomes: 𝑓 0.40 ( 12903 hom., cov: 29)

Consequence

IL19
NM_153758.5 intron

Scores

2

Clinical Significance

Uncertain risk allele no assertion criteria provided O:1

Conservation

PhyloP100: 0.0260

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL19NM_153758.5 linkuse as main transcriptc.-149+2474T>C intron_variant ENST00000659997.3
IL19NM_001393490.1 linkuse as main transcriptc.-149+2722T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL19ENST00000659997.3 linkuse as main transcriptc.-149+2474T>C intron_variant NM_153758.5 P1Q9UHD0-1

Frequencies

GnomAD3 genomes
AF:
0.401
AC:
60462
AN:
150900
Hom.:
12903
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.337
Gnomad AMI
AF:
0.443
Gnomad AMR
AF:
0.303
Gnomad ASJ
AF:
0.408
Gnomad EAS
AF:
0.0529
Gnomad SAS
AF:
0.250
Gnomad FIN
AF:
0.475
Gnomad MID
AF:
0.347
Gnomad NFE
AF:
0.487
Gnomad OTH
AF:
0.382
Alfa
AF:
0.453
Hom.:
32372
Bravo
AF:
0.387
Asia WGS
AF:
0.159
AC:
554
AN:
3478

ClinVar

Significance: Uncertain risk allele
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Leprosy, susceptibility to, 1 Other:1
Uncertain risk allele, no assertion criteria providedcase-controlCentro Dermatológico Federico Lleras Acosta, Hospital Universitario Centro Dermatológico Federico Lleras AcostaJun 10, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
5.4
Dann
Benign
0.80

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: rs1800896; hg19: chr1-206946897;