1-115339882-T-C

Variant names:

• chr1-115339882-T-C
• rs3811014
• ENST00000425449.1:n.208-25788T>C

Variant summary

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

The ENST00000425449.1(NGF-AS1):​n.208-25788T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,174 control chromosomes in the GnomAD database, including 7,174 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 0.27 (7174 hom., cov: 33)
• Consequence: NGF-AS1 ENST00000425449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425449.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NGF-AS1	NR_157569.1		n.208-25788T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NGF-AS1	ENST00000425449.1	TSL:2	n.208-25788T>C		intron	N/A
	NGF-AS1	ENST00000793538.1		n.501-25788T>C		intron	N/A
	NGF-AS1	ENST00000793539.1		n.253-25788T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40872 AN: 152056 Hom.: 7163 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.269 AC: 40930 AN: 152174 Hom.: 7174 Cov.: 33 AF XY: 0.266 AC XY: 19760 AN XY: 74414

African (AFR) AF: 0.500 AC: 20732 AN: 41486

American (AMR) AF: 0.170 AC: 2597 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3472

East Asian (EAS) AF: 0.161 AC: 833 AN: 5174

South Asian (SAS) AF: 0.233 AC: 1124 AN: 4826

European-Finnish (FIN) AF: 0.177 AC: 1879 AN: 10602

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.182 AC: 12349 AN: 68008

Other (OTH) AF: 0.232 AC: 490 AN: 2114

Alfa AF: 0.209 Hom.: 8637

Bravo AF: 0.276

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.50
DANN	Benign	0.28
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs3811014; hg19: chr1-115882503;