rs6947789

Positions:

• chr7-34411268-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

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

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-AS1	NR_033665.1	n.373+6311A>G		intron_variant, non_coding_transcript_variant
NPSR1-AS1	NR_033664.1	n.523+6311A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPSR1-AS1	ENST00000419766.5	n.485+6311A>G		intron_variant, non_coding_transcript_variant		1
NPSR1-AS1	ENST00000539747.5	n.404+6311A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30034 AN: 151964 Hom.: 3017 Cov.: 31

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

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

Other links and lift over

dbSNP: rs6947789; hg19: chr7-34450880;