rs10486643

Variant names:

• chr7-34489484-C-G
• rs10486643
• ENST00000419766.5:n.392-71812G>C

Variant summary

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

The ENST00000419766.5(NPSR1-AS1):​n.392-71812G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0586 in 152,226 control chromosomes in the GnomAD database, including 541 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 0.059 (541 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000419766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419766.5. 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.430-71812G>C		intron	N/A
	NPSR1-AS1	NR_033665.1		n.280-71812G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	ENST00000419766.5	TSL:1	n.392-71812G>C		intron	N/A
	NPSR1-AS1	ENST00000539747.5	TSL:2	n.311-71812G>C		intron	N/A
	NPSR1-AS1	ENST00000737194.1		n.392-71812G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0586 AC: 8908 AN: 152108 Hom.: 537 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.0191

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0586 AC: 8927 AN: 152226 Hom.: 541 Cov.: 32 AF XY: 0.0571 AC XY: 4246 AN XY: 74424

African (AFR) AF: 0.156 AC: 6469 AN: 41514

American (AMR) AF: 0.0235 AC: 360 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00547 AC: 19 AN: 3472

East Asian (EAS) AF: 0.0654 AC: 338 AN: 5168

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4818

European-Finnish (FIN) AF: 0.0245 AC: 260 AN: 10604

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0187 AC: 1270 AN: 68034

Other (OTH) AF: 0.0469 AC: 99 AN: 2112

Alfa AF: 0.0427 Hom.: 38

Bravo AF: 0.0628

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.49
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10486643; hg19: chr7-34529096;