rs2530545

Variant names:

• chr7-34657528-C-T
• rs2530545
• ENST00000358772.8:n.279+71209G>A

Variant summary

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

The ENST00000358772.8(NPSR1-AS1):​n.279+71209G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,064 control chromosomes in the GnomAD database, including 4,663 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 0.22 (4663 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 8 publications found

Genes affected

NPSR1-AS1 (HGNC:22128): (NPSR1 antisense RNA 1) This gene is located within a region that has been associated with asthma susceptibility. The locus is considered non-protein-coding based on lack of protein homology and a lack of experimental support for an encoded protein. Three alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, May 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPSR1-AS1	NR_033664.1	n.279+71209G>A		intron_variant	Intron 2 of 4
NPSR1-AS1	NR_033665.1	n.279+71209G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPSR1-AS1	ENST00000358772.8	n.279+71209G>A		intron_variant	Intron 2 of 3	1
NPSR1-AS1	ENST00000419766.5	n.241+71209G>A		intron_variant	Intron 2 of 4	1
NPSR1-AS1	ENST00000431669.5	n.245-14177G>A		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33802 AN: 151946 Hom.: 4659 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.223

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.222 AC: 33833 AN: 152064 Hom.: 4663 Cov.: 32 AF XY: 0.222 AC XY: 16519 AN XY: 74318

African (AFR) AF: 0.392 AC: 16229 AN: 41442

American (AMR) AF: 0.147 AC: 2252 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1014 AN: 5164

South Asian (SAS) AF: 0.156 AC: 748 AN: 4802

European-Finnish (FIN) AF: 0.172 AC: 1818 AN: 10572

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.154 AC: 10487 AN: 68008

Other (OTH) AF: 0.222 AC: 469 AN: 2108

Alfa AF: 0.205 Hom.: 3778

Bravo AF: 0.227

Asia WGS AF: 0.186 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.46
PhyloP100		-0.0010

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: rs2530545; hg19: chr7-34697140;