rs1800871

chr1-206773289-A-G

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 (★).

Frequency

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

Consequence

IL19
NM_153758 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.292

Links

IL19 (HGNC:5990):

IL10 (HGNC:5962):

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
IL19	NM_153758.5 linkuse as main transcript	c.-149+2211A>G		intron_variant		ENST00000659997.3
IL19	NM_001393490.1 linkuse as main transcript	c.-149+2459A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL19	ENST00000659997.3 linkuse as main transcript	c.-149+2211A>G		intron_variant			NM_153758.5	P1	Q9UHD0-1

Frequencies

GnomAD3 genomes

AF:

0.687

AC:

104313

AN:

151946

Hom.:

36709

Cov.:

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 submitter

clinical testing

Invitae

Nov 01, 2022

- -

Leprosy, susceptibility to, 1

Other:1

Uncertain risk allele, no assertion criteria provided

case-control

Centro Dermatológico Federico Lleras Acosta, Hospital Universitario Centro Dermatológico Federico Lleras Acosta

Jun 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over