chr13-48709659-A-G

Variant names:

• chr13-48709659-A-G
• rs2407249
• NM_001308476.3:c.*1801A>G

Variant summary

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

The NM_020377.5(CYSLTR2):​c.*1801A>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 0.163 in 152,210 control chromosomes in the GnomAD database, including 2,146 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 0.16 (2146 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CYSLTR2 NM_020377.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547
• Publications: 9 publications found

Genes affected

CYSLTR2 (HGNC:18274): (cysteinyl leukotriene receptor 2) The cysteinyl leukotrienes LTC4, LTD4, and LTE4 are important mediators of human bronchial asthma. Pharmacologic studies have determined that cysteinyl leukotrienes activate at least 2 receptors, the protein encoded by this gene and CYSLTR1. This encoded receptor is a member of the superfamily of G protein-coupled receptors. It seems to play a major role in endocrine and cardiovascular systems. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020377.5. 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
	CYSLTR2	NM_001308476.3	MANE Select	c.*1801A>G		3_prime_UTR	Exon 5 of 5	NP_001295405.1
	CYSLTR2	NM_001308465.3		c.*1801A>G		3_prime_UTR	Exon 6 of 6	NP_001295394.1
	CYSLTR2	NM_001308467.3		c.*1801A>G		3_prime_UTR	Exon 6 of 6	NP_001295396.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYSLTR2	ENST00000682523.1	MANE Select	c.*1801A>G		3_prime_UTR	Exon 5 of 5	ENSP00000508181.1
	CYSLTR2	ENST00000282018.4	TSL:6	c.*1801A>G		3_prime_UTR	Exon 1 of 1	ENSP00000282018.3
	CYSLTR2	ENST00000859943.1		c.*1801A>G		3_prime_UTR	Exon 3 of 3	ENSP00000530002.1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24746 AN: 152092 Hom.: 2143 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0803

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.176

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.163 AC: 24774 AN: 152210 Hom.: 2146 Cov.: 32 AF XY: 0.161 AC XY: 12013 AN XY: 74422

African (AFR) AF: 0.122 AC: 5051 AN: 41534

American (AMR) AF: 0.205 AC: 3140 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 824 AN: 3470

East Asian (EAS) AF: 0.0799 AC: 414 AN: 5184

South Asian (SAS) AF: 0.211 AC: 1017 AN: 4824

European-Finnish (FIN) AF: 0.129 AC: 1371 AN: 10602

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.182 AC: 12407 AN: 67998

Other (OTH) AF: 0.179 AC: 377 AN: 2106

Alfa AF: 0.177 Hom.: 9417

Bravo AF: 0.162

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.63
PhyloP100		0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2407249; hg19: chr13-49283795;