7-34589492-A-G

Variant names:

• chr7-34589492-A-G
• rs2893482
• ENST00000358772.8:n.280-19631T>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.280-19631T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,024 control chromosomes in the GnomAD database, including 11,717 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 (11717 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	NR_033664.1		n.280-19631T>C		intron	N/A
	NPSR1-AS1	NR_033665.1		n.279+139245T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	ENST00000358772.8	TSL:1	n.280-19631T>C		intron	N/A
	NPSR1-AS1	ENST00000419766.5	TSL:1	n.242-19631T>C		intron	N/A
	NPSR1-AS1	ENST00000439852.5	TSL:1	n.400-19631T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54478 AN: 151906 Hom.: 11672 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.359 AC: 54597 AN: 152024 Hom.: 11717 Cov.: 32 AF XY: 0.360 AC XY: 26719 AN XY: 74320

African (AFR) AF: 0.601 AC: 24898 AN: 41458

American (AMR) AF: 0.338 AC: 5161 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 897 AN: 3472

East Asian (EAS) AF: 0.448 AC: 2314 AN: 5162

South Asian (SAS) AF: 0.326 AC: 1567 AN: 4804

European-Finnish (FIN) AF: 0.222 AC: 2348 AN: 10572

Middle Eastern (MID) AF: 0.403 AC: 117 AN: 290

European-Non Finnish (NFE) AF: 0.241 AC: 16384 AN: 67982

Other (OTH) AF: 0.344 AC: 726 AN: 2110

Alfa AF: 0.308 Hom.: 1413

Bravo AF: 0.378

Asia WGS AF: 0.383 AC: 1328 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.9
DANN	Benign	0.46
PhyloP100		0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2893482;

hg19: chr7-34629104;