rs6973569

Variant names:

• chr7-34583412-G-A
• rs6973569
• ENST00000358772.8:n.280-13551C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-34583412-G-A
• chr7-34583412-G-T

Variant summary

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

The ENST00000358772.8(NPSR1-AS1):​n.280-13551C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.048 in 85,910 control chromosomes in the GnomAD database, including 80 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 0.048 (80 hom., cov: 24)
• Consequence: NPSR1-AS1 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPSR1-AS1	NR_033664.1	n.280-13551C>T		intron_variant	Intron 2 of 4
NPSR1-AS1	NR_033665.1	n.279+145325C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPSR1-AS1	ENST00000358772.8	n.280-13551C>T		intron_variant	Intron 2 of 3	1
NPSR1-AS1	ENST00000419766.5	n.242-13551C>T		intron_variant	Intron 2 of 4	1
NPSR1-AS1	ENST00000439852.5	n.400-13551C>T		intron_variant	Intron 3 of 5	1

Frequencies

GnomAD3 genomes AF: 0.0479 AC: 4119 AN: 85936 Hom.: 80 Cov.: 24

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.0100

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0745

Gnomad MID AF: 0.0417

Gnomad NFE AF: 0.0295

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0480 AC: 4121 AN: 85910 Hom.: 80 Cov.: 24 AF XY: 0.0499 AC XY: 2110 AN XY: 42272

African (AFR) AF: 0.116 AC: 1083 AN: 9376

American (AMR) AF: 0.0295 AC: 304 AN: 10318

Ashkenazi Jewish (ASJ) AF: 0.0100 AC: 23 AN: 2292

East Asian (EAS) AF: 0.0778 AC: 334 AN: 4292

South Asian (SAS) AF: 0.109 AC: 405 AN: 3702

European-Finnish (FIN) AF: 0.0745 AC: 502 AN: 6738

Middle Eastern (MID) AF: 0.0467 AC: 7 AN: 150

European-Non Finnish (NFE) AF: 0.0295 AC: 1393 AN: 47154

Other (OTH) AF: 0.0588 AC: 70 AN: 1190

Alfa AF: 0.177 Hom.: 3549

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.087
DANN	Benign	0.51
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6973569; hg19: chr7-34623024;