7-34657448-G-T

Variant names:

• chr7-34657448-G-T
• rs2530544
• ENST00000358772.8:n.279+71289C>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+71289C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,984 control chromosomes in the GnomAD database, including 5,815 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 0.26 (5815 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPSR1-AS1	NR_033664.1	n.279+71289C>A		intron_variant	Intron 2 of 4
NPSR1-AS1	NR_033665.1	n.279+71289C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPSR1-AS1	ENST00000358772.8	n.279+71289C>A		intron_variant	Intron 2 of 3	1
NPSR1-AS1	ENST00000419766.5	n.241+71289C>A		intron_variant	Intron 2 of 4	1
NPSR1-AS1	ENST00000431669.5	n.245-14097C>A		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39615 AN: 151868 Hom.: 5813 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.261 AC: 39641 AN: 151984 Hom.: 5815 Cov.: 32 AF XY: 0.260 AC XY: 19302 AN XY: 74278

African (AFR) AF: 0.400 AC: 16550 AN: 41420

American (AMR) AF: 0.184 AC: 2821 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 914 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5164

South Asian (SAS) AF: 0.168 AC: 809 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2443 AN: 10546

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14191 AN: 67966

Other (OTH) AF: 0.261 AC: 551 AN: 2108

Alfa AF: 0.226 Hom.: 11068

Bravo AF: 0.262

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.68
PhyloP100		0.15

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: rs2530544; hg19: chr7-34697060;