7-34598402-C-T

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+130335G>A 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 0.357 in 151,906 control chromosomes in the GnomAD database, including 11,484 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 0.36 (11484 hom., cov: 32)
• Consequence: NPSR1-AS1 NR_033665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPSR1-AS1	NR_033665.1	n.279+130335G>A		intron_variant, non_coding_transcript_variant
NPSR1-AS1	NR_033664.1	n.280-28541G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPSR1-AS1	ENST00000358772.8	n.280-28541G>A		intron_variant, non_coding_transcript_variant		1
NPSR1-AS1	ENST00000419766.5	n.242-28541G>A		intron_variant, non_coding_transcript_variant		1
NPSR1-AS1	ENST00000439852.5	n.400-28541G>A		intron_variant, non_coding_transcript_variant		1
NPSR1-AS1	ENST00000539747.5	n.161-28541G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54103 AN: 151788 Hom.: 11442 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.357 AC: 54218 AN: 151906 Hom.: 11484 Cov.: 32 AF XY: 0.357 AC XY: 26530 AN XY: 74242

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.343

Alfa AF: 0.272 Hom.: 2964

Bravo AF: 0.376

Asia WGS AF: 0.386 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.38
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6462569; hg19: chr7-34638014;