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GeneBe

rs1800871

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_153758(IL19):c.-149+2211A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 151946 control chromosomes in the gnomAD Genomes database, including 36709 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (‚ėÖ).

Frequency

Genomes: ūĚĎď 0.69 ( 36709 hom., cov: 31)

Consequence

IL19
NM_153758 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: -0.292

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
?
Variant 1:206773289-A>G is Benign according to our data. Variant chr1-206773289-A-G is described in ClinVar as [Benign]. Clinvar id is 1166836. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL19NM_153758.5 linkuse as main transcriptc.-149+2211A>G intron_variant ENST00000659997.3
IL19NM_001393490.1 linkuse as main transcriptc.-149+2459A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL19ENST00000659997.3 linkuse as main transcriptc.-149+2211A>G intron_variant NM_153758.5 P1Q9UHD0-1

Frequencies

GnomAD3 genomes
AF:
0.687
AC:
104313
AN:
151946
Hom.:
36709
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.589
Gnomad AMI
AF:
0.707
Gnomad AMR
AF:
0.674
Gnomad ASJ
AF:
0.750
Gnomad EAS
AF:
0.315
Gnomad SAS
AF:
0.564
Gnomad FIN
AF:
0.776
Gnomad MID
AF:
0.688
Gnomad NFE
AF:
0.768
Gnomad OTH
AF:
0.679
Alfa
AF:
0.737
Hom.:
80969
Bravo
AF:
0.674
Asia WGS
AF:
0.488
AC:
1703
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inflammatory bowel disease Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeNov 01, 2022- -
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
-0.93
Cadd
Benign
1.3
Dann
Benign
0.32

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: rs1800871; hg19: chr1-206946634;