rs6462563

Variant names:

• chr7-34511167-G-C
• rs6462563
• ENST00000419766.5:n.391+58545C>G

Variant summary

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

The ENST00000419766.5(NPSR1-AS1):​n.391+58545C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 152,256 control chromosomes in the GnomAD database, including 88 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 0.027 (88 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000419766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 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.429+58545C>G		intron	N/A
	NPSR1-AS1	NR_033665.1		n.280-93495C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	ENST00000419766.5	TSL:1	n.391+58545C>G		intron	N/A
	NPSR1-AS1	ENST00000539747.5	TSL:2	n.310+58545C>G		intron	N/A
	NPSR1-AS1	ENST00000737194.1		n.391+58545C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0269 AC: 4093 AN: 152138 Hom.: 88 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.0489

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0231

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0269 AC: 4092 AN: 152256 Hom.: 88 Cov.: 32 AF XY: 0.0290 AC XY: 2159 AN XY: 74424

African (AFR) AF: 0.0134 AC: 555 AN: 41572

American (AMR) AF: 0.0194 AC: 297 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00836 AC: 29 AN: 3470

East Asian (EAS) AF: 0.117 AC: 604 AN: 5180

South Asian (SAS) AF: 0.0878 AC: 423 AN: 4820

European-Finnish (FIN) AF: 0.0489 AC: 518 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0231 AC: 1573 AN: 68008

Other (OTH) AF: 0.0341 AC: 72 AN: 2112

Alfa AF: 0.0274 Hom.: 7

Bravo AF: 0.0214

Asia WGS AF: 0.0970 AC: 334 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		0.27

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: rs6462563;

hg19: chr7-34550779;