chr5-111076887-A-G

Variant names:

• chr5-111076887-A-G
• rs11466749
• NM_033035.5:c.*813A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033035.5(TSLP):​c.*813A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,134 control chromosomes in the GnomAD database, including 1,776 homozygotes. 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 0.15 (1775 hom., cov: 32)
  • Exomes 𝑓: 0.21 (1 hom.)
• Consequence: TSLP NM_033035.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• Publications: 35 publications found

Genes affected

TSLP (HGNC:30743): (thymic stromal lymphopoietin) This gene encodes a hemopoietic cytokine proposed to signal through a heterodimeric receptor complex composed of the thymic stromal lymphopoietin receptor and the IL-7R alpha chain. It mainly impacts myeloid cells and induces the release of T cell-attracting chemokines from monocytes and enhances the maturation of CD11c(+) dendritic cells. The protein promotes T helper type 2 (TH2) cell responses that are associated with immunity in various inflammatory diseases, including asthma, allergic inflammation and chronic obstructive pulmonary disease. The protein is therefore considered a potential therapeutic target for the treatment of such diseases. In addition, the shorter (predominant) isoform is an antimicrobial protein, displaying antibacterial and antifungal activity against B. cereus, E. coli, E. faecalis, S. mitis, S. epidermidis, and C. albicans. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2020]

ENSG00000253613 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033035.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSLP	NM_033035.5	MANE Select	c.*813A>G		3_prime_UTR	Exon 4 of 4	NP_149024.1
	TSLP	NR_045089.2		n.2715A>G		non_coding_transcript_exon	Exon 5 of 5
	TSLP	NM_138551.5		c.*813A>G		3_prime_UTR	Exon 2 of 2	NP_612561.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSLP	ENST00000344895.4	TSL:1 MANE Select	c.*813A>G		3_prime_UTR	Exon 4 of 4	ENSP00000339804.3
	TSLP	ENST00000379706.4	TSL:1	c.*813A>G		3_prime_UTR	Exon 2 of 2	ENSP00000427827.1
	ENSG00000253613	ENST00000741219.1		n.261+34T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22430 AN: 152002 Hom.: 1774 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0986

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0682

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.138

GnomAD4 exome AF: 0.214 AC: 3 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 3 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.148 AC: 22440 AN: 152120 Hom.: 1775 Cov.: 32 AF XY: 0.148 AC XY: 10998 AN XY: 74362

African (AFR) AF: 0.113 AC: 4695 AN: 41504

American (AMR) AF: 0.0984 AC: 1503 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3470

East Asian (EAS) AF: 0.0683 AC: 354 AN: 5180

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4820

European-Finnish (FIN) AF: 0.182 AC: 1929 AN: 10580

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11786 AN: 67982

Other (OTH) AF: 0.138 AC: 291 AN: 2102

Alfa AF: 0.152 Hom.: 2412

Bravo AF: 0.132

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.51
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11466749; hg19: chr5-110412585;