7-34656933-C-T

Variant names:

• chr7-34656933-C-T
• rs1023556
• ENST00000358772.8:n.279+71804G>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+71804G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,054 control chromosomes in the GnomAD database, including 8,893 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 0.32 (8893 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPSR1-AS1	NR_033664.1	n.279+71804G>A		intron_variant	Intron 2 of 4
NPSR1-AS1	NR_033665.1	n.279+71804G>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+71804G>A		intron_variant	Intron 2 of 3	1
NPSR1-AS1	ENST00000419766.5	n.241+71804G>A		intron_variant	Intron 2 of 4	1
NPSR1-AS1	ENST00000431669.5	n.245-13582G>A		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49181 AN: 151936 Hom.: 8880 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.324 AC: 49234 AN: 152054 Hom.: 8893 Cov.: 32 AF XY: 0.327 AC XY: 24294 AN XY: 74346

African (AFR) AF: 0.475 AC: 19693 AN: 41420

American (AMR) AF: 0.330 AC: 5041 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3468

East Asian (EAS) AF: 0.493 AC: 2552 AN: 5174

South Asian (SAS) AF: 0.325 AC: 1564 AN: 4818

European-Finnish (FIN) AF: 0.222 AC: 2352 AN: 10590

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16132 AN: 67978

Other (OTH) AF: 0.315 AC: 666 AN: 2112

Alfa AF: 0.259 Hom.: 9488

Bravo AF: 0.338

Asia WGS AF: 0.383 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.033
DANN	Benign	0.56
PhyloP100		-2.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1023556; hg19: chr7-34696545;