rs6947789

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_033665.1(NPSR1-AS1):​n.373+6311A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,080 control chromosomes in the GnomAD database, including 3,024 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 0.20 ( 3024 hom., cov: 31)

Consequence

NPSR1-AS1
NR_033665.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.136
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NPSR1-AS1NR_033665.1 linkuse as main transcriptn.373+6311A>G intron_variant, non_coding_transcript_variant
NPSR1-AS1NR_033664.1 linkuse as main transcriptn.523+6311A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NPSR1-AS1ENST00000419766.5 linkuse as main transcriptn.485+6311A>G intron_variant, non_coding_transcript_variant 1
NPSR1-AS1ENST00000539747.5 linkuse as main transcriptn.404+6311A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.198
AC:
30034
AN:
151964
Hom.:
3017
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.214
Gnomad AMI
AF:
0.251
Gnomad AMR
AF:
0.184
Gnomad ASJ
AF:
0.210
Gnomad EAS
AF:
0.178
Gnomad SAS
AF:
0.296
Gnomad FIN
AF:
0.200
Gnomad MID
AF:
0.193
Gnomad NFE
AF:
0.184
Gnomad OTH
AF:
0.203
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.198
AC:
30047
AN:
152080
Hom.:
3024
Cov.:
31
AF XY:
0.200
AC XY:
14850
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.214
Gnomad4 AMR
AF:
0.183
Gnomad4 ASJ
AF:
0.210
Gnomad4 EAS
AF:
0.178
Gnomad4 SAS
AF:
0.297
Gnomad4 FIN
AF:
0.200
Gnomad4 NFE
AF:
0.184
Gnomad4 OTH
AF:
0.204
Alfa
AF:
0.188
Hom.:
5657
Bravo
AF:
0.194
Asia WGS
AF:
0.229
AC:
795
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.3
DANN
Benign
0.55

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6947789; hg19: chr7-34450880; API