rs10489531

Variant names:

• chr1-115240381-G-A
• rs10489531
• ENST00000793538.1:n.82+475G>A

Variant summary

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

The ENST00000793538.1(NGF-AS1):​n.82+475G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,106 control chromosomes in the GnomAD database, including 5,714 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 0.24 (5714 hom., cov: 32)
• Consequence: NGF-AS1 ENST00000793538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 4 publications found

Genes affected

NGF-AS1 (HGNC:53922): (NGF antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793538.1. 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
	NGF-AS1	ENST00000793538.1		n.82+475G>A		intron	N/A
	NGF-AS1	ENST00000793543.1		n.369+475G>A		intron	N/A
	NGF-AS1	ENST00000793545.1		n.*33G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36510 AN: 151986 Hom.: 5716 Cov.: 32

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.240 AC: 36497 AN: 152106 Hom.: 5714 Cov.: 32 AF XY: 0.233 AC XY: 17341 AN XY: 74330

African (AFR) AF: 0.0719 AC: 2984 AN: 41528

American (AMR) AF: 0.205 AC: 3135 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5172

South Asian (SAS) AF: 0.163 AC: 786 AN: 4812

European-Finnish (FIN) AF: 0.310 AC: 3277 AN: 10570

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24107 AN: 67962

Other (OTH) AF: 0.260 AC: 550 AN: 2112

Alfa AF: 0.319 Hom.: 4319

Bravo AF: 0.225

Asia WGS AF: 0.0800 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.61
PhyloP100		-0.36

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: rs10489531;

hg19: chr1-115783002;