rs714588

Variant names:

• chr7-34653614-A-G
• rs714588
• ENST00000358772.8:n.279+75123T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-34653614-A-G
• chr7-34653614-A-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.279+75123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,036 control chromosomes in the GnomAD database, including 16,583 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 0.46 (16583 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPSR1-AS1	NR_033664.1	n.279+75123T>C		intron_variant	Intron 2 of 4
NPSR1-AS1	NR_033665.1	n.279+75123T>C		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+75123T>C		intron_variant	Intron 2 of 3	1
NPSR1-AS1	ENST00000419766.5	n.241+75123T>C		intron_variant	Intron 2 of 4	1
NPSR1-AS1	ENST00000431669.5	n.245-10263T>C		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70322 AN: 151918 Hom.: 16567 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.463 AC: 70382 AN: 152036 Hom.: 16583 Cov.: 32 AF XY: 0.464 AC XY: 34472 AN XY: 74304

African (AFR) AF: 0.543 AC: 22513 AN: 41466

American (AMR) AF: 0.451 AC: 6887 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1545 AN: 5164

South Asian (SAS) AF: 0.480 AC: 2314 AN: 4820

European-Finnish (FIN) AF: 0.441 AC: 4669 AN: 10576

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29415 AN: 67956

Other (OTH) AF: 0.480 AC: 1010 AN: 2102

Alfa AF: 0.441 Hom.: 40485

Bravo AF: 0.464

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.63
DANN	Benign	0.54
PhyloP100		-0.70

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: rs714588; hg19: chr7-34693226;