rs1800925

Variant summary

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

The ENST00000435042(TH2LCRR):n.94+7062G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152002 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 0.0000066 ( 0 hom., cov: 32)

Consequence

TH2LCRR
ENST00000435042 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.487

Links

TH2LCRR (HGNC:40495):

IL13 (HGNC:5973):

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 = 0.00000658 (1/152002) while in subpopulation NFE AF= 0.0000147 (1/68006). AF 95% confidence interval is 0. There are 0 homozygotes in gnomad. There are 0 alleles in male gnomad subpopulation. Median coverage is 32. This position pass quality control queck.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
IL13	NM_001354992.2 linkuse as main transcript	c.-220C>G	5_prime_UTR_variant	2/6
IL13	NM_001354993.2 linkuse as main transcript	c.-149C>G	5_prime_UTR_variant	2/5
IL13	NM_001354991.2 linkuse as main transcript	c.-93+487C>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
TH2LCRR	ENST00000435042.1 linkuse as main transcript	n.94+7062G>C	intron_variant, non_coding_transcript_variant		5
IL13	ENST00000468334.5 linkuse as main transcript	n.420C>G	non_coding_transcript_exon_variant	2/5	3
IL13	ENST00000487267.5 linkuse as main transcript	n.147C>G	non_coding_transcript_exon_variant	2/6	3
IL13	ENST00000459878.5 linkuse as main transcript	n.107+487C>G	intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00000658

AC:

AN:

152002

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

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:

0.0000147

Gnomad OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

Cadd

Benign

7.4

Dann

Benign

0.34

Splicing

Find out SpliceAI 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

Computational scores

Splicing

Publications

LitVar

Other links and lift over