ENST00000660587.2:n.181-2100C>T

Variant names:

• chr7-34295479-C-T
• rs2058163
• ENST00000660587.2:n.181-2100C>T

Variant summary

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

The ENST00000660587.2(ENSG00000236212):​n.181-2100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,776 control chromosomes in the GnomAD database, including 10,708 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 0.37 (10708 hom., cov: 32)
• Consequence: ENSG00000236212 ENST00000660587.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 4 publications found

Genes affected

ENSG00000236212 (HGNC:):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236212	ENST00000660587.2	n.181-2100C>T		intron_variant	Intron 1 of 1
NPSR1-AS1	ENST00000737198.1	n.95-8032G>A		intron_variant	Intron 1 of 1
ENSG00000236212	ENST00000737263.1	n.161-2100C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56666 AN: 151658 Hom.: 10686 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.374 AC: 56731 AN: 151776 Hom.: 10708 Cov.: 32 AF XY: 0.374 AC XY: 27690 AN XY: 74134

African (AFR) AF: 0.364 AC: 15063 AN: 41380

American (AMR) AF: 0.444 AC: 6768 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3468

East Asian (EAS) AF: 0.439 AC: 2259 AN: 5140

South Asian (SAS) AF: 0.259 AC: 1243 AN: 4804

European-Finnish (FIN) AF: 0.352 AC: 3704 AN: 10514

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25280 AN: 67910

Other (OTH) AF: 0.389 AC: 823 AN: 2114

Alfa AF: 0.369 Hom.: 6296

Bravo AF: 0.384

Asia WGS AF: 0.364 AC: 1267 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2058163; hg19: chr7-34335091;