rs1006392

Variant names:

• chr7-34651330-C-G
• rs1006392
• ENST00000358772.8:n.279+77407G>C

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+77407G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,934 control chromosomes in the GnomAD database, including 29,227 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 0.61 (29227 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000358772.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	NR_033664.1		n.279+77407G>C		intron	N/A
	NPSR1-AS1	NR_033665.1		n.279+77407G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	ENST00000358772.8	TSL:1	n.279+77407G>C		intron	N/A
	NPSR1-AS1	ENST00000419766.5	TSL:1	n.241+77407G>C		intron	N/A
	NPSR1-AS1	ENST00000431669.5	TSL:1	n.245-7979G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93302 AN: 151816 Hom.: 29189 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.615 AC: 93396 AN: 151934 Hom.: 29227 Cov.: 32 AF XY: 0.619 AC XY: 45941 AN XY: 74236

African (AFR) AF: 0.691 AC: 28627 AN: 41458

American (AMR) AF: 0.664 AC: 10146 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1860 AN: 3462

East Asian (EAS) AF: 0.757 AC: 3914 AN: 5168

South Asian (SAS) AF: 0.708 AC: 3414 AN: 4820

European-Finnish (FIN) AF: 0.546 AC: 5746 AN: 10520

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37721 AN: 67920

Other (OTH) AF: 0.608 AC: 1286 AN: 2114

Alfa AF: 0.574 Hom.: 3164

Bravo AF: 0.627

Asia WGS AF: 0.710 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.44
PhyloP100		-0.52

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: rs1006392; hg19: chr7-34690942;