7-34657860-C-T

Variant names:

• chr7-34657860-C-T
• rs2168890
• ENST00000358772.8:n.279+70877G>A

Variant summary

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

The ENST00000358772.8(NPSR1-AS1):​n.279+70877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,108 control chromosomes in the GnomAD database, including 3,791 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 0.19 (3791 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	NR_033664.1		n.279+70877G>A		intron	N/A
	NPSR1-AS1	NR_033665.1		n.279+70877G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	ENST00000358772.8	TSL:1	n.279+70877G>A		intron	N/A
	NPSR1-AS1	ENST00000419766.5	TSL:1	n.241+70877G>A		intron	N/A
	NPSR1-AS1	ENST00000431669.5	TSL:1	n.245-14509G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29088 AN: 151990 Hom.: 3789 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0724

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.191 AC: 29126 AN: 152108 Hom.: 3791 Cov.: 32 AF XY: 0.187 AC XY: 13926 AN XY: 74366

African (AFR) AF: 0.370 AC: 15335 AN: 41466

American (AMR) AF: 0.137 AC: 2093 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3472

East Asian (EAS) AF: 0.0211 AC: 109 AN: 5176

South Asian (SAS) AF: 0.0723 AC: 349 AN: 4830

European-Finnish (FIN) AF: 0.0930 AC: 984 AN: 10580

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9069 AN: 67984

Other (OTH) AF: 0.194 AC: 410 AN: 2108

Alfa AF: 0.0649 Hom.: 78

Bravo AF: 0.204

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.41
PromoterAI		-0.020	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2168890; hg19: chr7-34697472;