rs1800872

chr1-206773062-T-G

Variant summary

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

The NM_153758(IL19):c.-149+1984T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 151940 control chromosomes in the gnomAD Genomes database, including 36691 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.69 ( 36691 hom., cov: 31)

Consequence

IL19
NM_153758 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:2O:2

Conservation

PhyloP100: 0.260

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=-0.81).

BP6

Variant 1:206773062-T>G is Benign according to our data. Variant chr1-206773062-T-G is described in ClinVar as [Benign]. Clinvar id is 16873. 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+1984T>G		intron_variant		ENST00000659997.3
IL19	NM_001393490.1 linkuse as main transcript	c.-149+2232T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL19	ENST00000659997.3 linkuse as main transcript	c.-149+1984T>G		intron_variant			NM_153758.5	P1	Q9UHD0-1

Frequencies

GnomAD3 genomes

AF:

0.686

AC:

104271

AN:

151940

Hom.:

36691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.588

Gnomad AMI

AF:

0.709

Gnomad AMR

AF:

0.674

Gnomad ASJ

AF:

0.749

Gnomad EAS

AF:

0.314

Gnomad SAS

AF:

0.563

Gnomad FIN

AF:

0.776

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.768

Gnomad OTH

AF:

0.678

Alfa

AF:

0.706

Hom.:

6316

Bravo

AF:

0.674

Asia WGS

AF:

0.488

AC:

1701

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2Other:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Graft-versus-host disease, resistance to

Benign:1

protective, no assertion criteria provided

literature only

OMIM

Dec 04, 2003

- -

Inflammatory bowel disease

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Nov 01, 2022

- -

Susceptibility to HIV infection

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Dec 04, 2003

- -

Cholangiocarcinoma

Other:1

other, no assertion criteria provided

research

Department of Surgery, Campus Charité Mitte Campus Virchow-klinikum, Charite-Universitaetsmedizin Berlin

Dec 10, 2022

No association with disease-free or overall survival after resection of intrahepatic Cholangiocarcinoma No association with disease-free or overall survival

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

Cadd

Benign

5.5

Dann

Benign

0.70

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