chr7-34411605-T-C

Position:

• chr7-34411605-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033665.1(NPSR1-AS1):​n.373+5974A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,894 control chromosomes in the GnomAD database, including 23,556 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 0.54 (23556 hom., cov: 31)
• Consequence: NPSR1-AS1 NR_033665.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPSR1-AS1	NR_033665.1	n.373+5974A>G		intron_variant, non_coding_transcript_variant
NPSR1-AS1	NR_033664.1	n.523+5974A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPSR1-AS1	ENST00000419766.5	n.485+5974A>G		intron_variant, non_coding_transcript_variant		1
NPSR1-AS1	ENST00000539747.5	n.404+5974A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82450 AN: 151776 Hom.: 23513 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.543 AC: 82551 AN: 151894 Hom.: 23556 Cov.: 31 AF XY: 0.543 AC XY: 40320 AN XY: 74250

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.513

Alfa AF: 0.470 Hom.: 34386

Bravo AF: 0.551

Asia WGS AF: 0.463 AC: 1613 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	12
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs736295; hg19: chr7-34451217;