7-34589492-A-G

Position:

• chr7-34589492-A-G

Variant summary

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

The ENST00000358772.8(NPSR1-AS1):​n.280-19631T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,024 control chromosomes in the GnomAD database, including 11,717 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 (11717 hom., cov: 32)
• Consequence: NPSR1-AS1 ENST00000358772.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226

Genes affected

NPSR1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NPSR1-AS1	NR_033664.1	n.280-19631T>C		intron_variant
NPSR1-AS1	NR_033665.1	n.279+139245T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NPSR1-AS1	ENST00000358772.8	n.280-19631T>C		intron_variant		1
NPSR1-AS1	ENST00000419766.5	n.242-19631T>C		intron_variant		1
NPSR1-AS1	ENST00000439852.5	n.400-19631T>C		intron_variant		1
NPSR1-AS1	ENST00000539747.5	n.161-19631T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54478 AN: 151906 Hom.: 11672 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.359 AC: 54597 AN: 152024 Hom.: 11717 Cov.: 32 AF XY: 0.360 AC XY: 26719 AN XY: 74320

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.344

Alfa AF: 0.308 Hom.: 1413

Bravo AF: 0.378

Asia WGS AF: 0.383 AC: 1328 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.9
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2893482; hg19: chr7-34629104;