rs10258145

Variant names:

• chr7-34560109-G-A
• rs10258145
• ENST00000419766.5:n.391+9603C>T

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+9603C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,352 control chromosomes in the GnomAD database, including 11,693 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 0.36 (11693 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000419766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPSR1-AS1	NR_033664.1	n.429+9603C>T		intron_variant	Intron 3 of 4
NPSR1-AS1	NR_033665.1	n.280-142437C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPSR1-AS1	ENST00000419766.5	n.391+9603C>T		intron_variant	Intron 3 of 4	1
NPSR1-AS1	ENST00000539747.5	n.310+9603C>T		intron_variant	Intron 3 of 4	2
NPSR1-AS1	ENST00000737194.1	n.391+9603C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54129 AN: 151234 Hom.: 11649 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.358 AC: 54247 AN: 151352 Hom.: 11693 Cov.: 32 AF XY: 0.358 AC XY: 26521 AN XY: 74030

African (AFR) AF: 0.603 AC: 24668 AN: 40878

American (AMR) AF: 0.344 AC: 5233 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 894 AN: 3464

East Asian (EAS) AF: 0.417 AC: 2155 AN: 5168

South Asian (SAS) AF: 0.326 AC: 1574 AN: 4828

European-Finnish (FIN) AF: 0.210 AC: 2215 AN: 10566

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16470 AN: 67918

Other (OTH) AF: 0.347 AC: 729 AN: 2098

Alfa AF: 0.323 Hom.: 1608

Bravo AF: 0.380

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.71
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10258145; hg19: chr7-34599721;