7-34566724-G-T

Variant names:

• chr7-34566724-G-T
• rs12690808
• ENST00000439852.5:n.709C>A

Variant summary

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

The ENST00000439852.5(NPSR1-AS1):​n.709C>A variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,998 control chromosomes in the GnomAD database, including 11,889 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 0.36 (11889 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: NPSR1-AS1 ENST00000439852.5 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439852.5. 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
	NPSR1-AS1	NR_033664.1		n.429+2988C>A		intron	N/A
	NPSR1-AS1	NR_033665.1		n.280-149052C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NPSR1-AS1	ENST00000439852.5	TSL:1	n.709C>A		splice_region non_coding_transcript_exon	Exon 6 of 6
	NPSR1-AS1	ENST00000419766.5	TSL:1	n.391+2988C>A		intron	N/A
	NPSR1-AS1	ENST00000539747.5	TSL:2	n.310+2988C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54829 AN: 151880 Hom.: 11844 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.349

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.361 AC: 54947 AN: 151998 Hom.: 11889 Cov.: 32 AF XY: 0.362 AC XY: 26876 AN XY: 74306

African (AFR) AF: 0.608 AC: 25176 AN: 41442

American (AMR) AF: 0.340 AC: 5189 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2315 AN: 5168

South Asian (SAS) AF: 0.327 AC: 1574 AN: 4820

European-Finnish (FIN) AF: 0.224 AC: 2370 AN: 10560

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16382 AN: 67962

Other (OTH) AF: 0.349 AC: 738 AN: 2114

Alfa AF: 0.323 Hom.: 1604

Bravo AF: 0.380

Asia WGS AF: 0.385 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.44
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs12690808; hg19: chr7-34606336;