rs2530543

chr7-34656347-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033665.1(NPSR1-AS1):n.279+72390A>G 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 0.265 in 152,082 control chromosomes in the GnomAD database, including 6,304 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 0.27 (6304 hom., cov: 32)
• Consequence: NPSR1-AS1 NR_033665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPSR1-AS1	NR_033665.1	n.279+72390A>G		intron_variant, non_coding_transcript_variant
NPSR1-AS1	NR_033664.1	n.279+72390A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPSR1-AS1	ENST00000419766.5	n.241+72390A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40272 AN: 151964 Hom.: 6298 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.265 AC: 40308 AN: 152082 Hom.: 6304 Cov.: 32 AF XY: 0.263 AC XY: 19556 AN XY: 74348

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.258

Alfa AF: 0.210 Hom.: 5979

Bravo AF: 0.271

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.9
Dann	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs2530543; hg19: chr7-34695959;