rs2609234

Variant names:

• chr7-34648813-G-A
• rs2609234
• ENST00000358772.8:n.280-78952C>T

Variant summary

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

The ENST00000358772.8(NPSR1-AS1):​n.280-78952C>T variant causes a intron 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 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 7 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=-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 rank	MANE	Protein	UniProt
NPSR1-AS1	NR_033664.1	n.280-78952C>T		intron_variant	Intron 2 of 4
NPSR1-AS1	NR_033665.1	n.279+79924C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPSR1-AS1	ENST00000358772.8	n.280-78952C>T		intron_variant	Intron 2 of 3	1
NPSR1-AS1	ENST00000419766.5	n.242-78952C>T		intron_variant	Intron 2 of 4	1
NPSR1-AS1	ENST00000431669.5	n.245-5462C>T		intron_variant	Intron 3 of 3	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

African (AFR) AF: 0.463 AC: 19167 AN: 41390

American (AMR) AF: 0.165 AC: 2511 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3466

East Asian (EAS) AF: 0.127 AC: 658 AN: 5164

South Asian (SAS) AF: 0.195 AC: 938 AN: 4814

European-Finnish (FIN) AF: 0.179 AC: 1888 AN: 10528

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11525 AN: 67860

Other (OTH) AF: 0.248 AC: 522 AN: 2104

Alfa AF: 0.199 Hom.: 8715

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
PhyloP100		-1.5

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: rs2609234; hg19: chr7-34688425;