7-34315488-C-T

Variant names:

• chr7-34315488-C-T
• rs1419842
• ENST00000737198.1:n.95-28041G>A

Variant summary

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

The ENST00000737198.1(NPSR1-AS1):​n.95-28041G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,904 control chromosomes in the GnomAD database, including 11,993 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 0.40 (11993 hom., cov: 31)
• Consequence: NPSR1-AS1 ENST00000737198.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737198.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	ENST00000737198.1		n.95-28041G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60276 AN: 151786 Hom.: 11980 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.397 AC: 60315 AN: 151904 Hom.: 11993 Cov.: 31 AF XY: 0.397 AC XY: 29476 AN XY: 74250

African (AFR) AF: 0.410 AC: 16987 AN: 41414

American (AMR) AF: 0.431 AC: 6586 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1327 AN: 3466

East Asian (EAS) AF: 0.336 AC: 1726 AN: 5134

South Asian (SAS) AF: 0.304 AC: 1463 AN: 4806

European-Finnish (FIN) AF: 0.383 AC: 4041 AN: 10554

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26895 AN: 67938

Other (OTH) AF: 0.408 AC: 861 AN: 2110

Alfa AF: 0.369 Hom.: 5754

Bravo AF: 0.402

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		-0.033

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1419842;

hg19: chr7-34355100;