rs2392268

Positions:

• chr7-34374815-A-G

Variant summary

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

The NR_033665.1(NPSR1-AS1):​n.374-23968T>C 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 0.303 in 152,070 control chromosomes in the GnomAD database, including 9,588 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 0.30 (9588 hom., cov: 33)
• Consequence: NPSR1-AS1 NR_033665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPSR1-AS1	NR_033665.1	n.374-23968T>C		intron_variant, non_coding_transcript_variant
NPSR1-AS1	NR_033664.1	n.524-23968T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPSR1-AS1	ENST00000419766.5	n.486-23968T>C		intron_variant, non_coding_transcript_variant		1
NPSR1-AS1	ENST00000539747.5	n.405-23968T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46044 AN: 151952 Hom.: 9575 Cov.: 33

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.303 AC: 46094 AN: 152070 Hom.: 9588 Cov.: 33 AF XY: 0.304 AC XY: 22577 AN XY: 74344

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.290

Alfa AF: 0.215 Hom.: 2168

Bravo AF: 0.319

Asia WGS AF: 0.425 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2392268; hg19: chr7-34414427;