rs2609234

Positions:

• chr7-34648813-G-A

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+79924C>T 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 0.251 in 151,750 control chromosomes in the GnomAD database, including 6,065 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 0.25 (6065 hom., cov: 32)
• Consequence: NPSR1-AS1 NR_033665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPSR1-AS1	NR_033665.1	n.279+79924C>T		intron_variant, non_coding_transcript_variant
NPSR1-AS1	NR_033664.1	n.280-78952C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPSR1-AS1	ENST00000419766.5	n.242-78952C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38071 AN: 151632 Hom.: 6054 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.251 AC: 38120 AN: 151750 Hom.: 6065 Cov.: 32 AF XY: 0.249 AC XY: 18500 AN XY: 74166

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.248

Alfa AF: 0.179 Hom.: 3643

Bravo AF: 0.257

Asia WGS AF: 0.186 AC: 645 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.15

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: rs2609234; hg19: chr7-34688425;