ENST00000419766.5:n.486-23968T>C

Variant names:

• chr7-34374815-A-G
• rs2392268
• ENST00000419766.5:n.486-23968T>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.486-23968T>C variant causes a intron 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 ENST00000419766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 1 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=-0.85).
• 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 rank	MANE	Protein	UniProt
NPSR1-AS1	NR_033664.1	n.524-23968T>C		intron_variant	Intron 4 of 4
NPSR1-AS1	NR_033665.1	n.374-23968T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPSR1-AS1	ENST00000419766.5	n.486-23968T>C		intron_variant	Intron 4 of 4	1
NPSR1-AS1	ENST00000539747.5	n.405-23968T>C		intron_variant	Intron 4 of 4	2
NPSR1-AS1	ENST00000737198.1	n.94+42764T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.578 AC: 23955 AN: 41450

American (AMR) AF: 0.223 AC: 3397 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2203 AN: 5168

South Asian (SAS) AF: 0.413 AC: 1989 AN: 4816

European-Finnish (FIN) AF: 0.146 AC: 1547 AN: 10600

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.171 AC: 11624 AN: 67984

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.216 Hom.: 2455

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2392268; hg19: chr7-34414427;