rs10237930

Variant names:

• chr7-34641608-T-C
• rs10237930
• ENST00000358772.8:n.280-71747A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-34641608-T-C
• chr7-34641608-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000358772.8(NPSR1-AS1):​n.280-71747A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,970 control chromosomes in the GnomAD database, including 18,643 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 0.49 (18643 hom., cov: 31)
• Consequence: NPSR1-AS1 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000358772.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	NR_033664.1		n.280-71747A>G		intron	N/A
	NPSR1-AS1	NR_033665.1		n.279+87129A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	ENST00000358772.8	TSL:1	n.280-71747A>G		intron	N/A
	NPSR1-AS1	ENST00000419766.5	TSL:1	n.242-71747A>G		intron	N/A
	NPSR1-AS1	ENST00000439852.5	TSL:1	n.399+62472A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74543 AN: 151850 Hom.: 18623 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.491 AC: 74606 AN: 151970 Hom.: 18643 Cov.: 31 AF XY: 0.489 AC XY: 36348 AN XY: 74280

African (AFR) AF: 0.562 AC: 23276 AN: 41442

American (AMR) AF: 0.471 AC: 7196 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1626 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1290 AN: 5164

South Asian (SAS) AF: 0.484 AC: 2333 AN: 4816

European-Finnish (FIN) AF: 0.459 AC: 4846 AN: 10548

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32459 AN: 67958

Other (OTH) AF: 0.497 AC: 1047 AN: 2108

Alfa AF: 0.480 Hom.: 9075

Bravo AF: 0.492

Asia WGS AF: 0.390 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.094
DANN	Benign	0.61
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10237930; hg19: chr7-34681220;