chr1-115280766-G-A

Variant names:

• chr1-115280766-G-A
• rs7523086
• ENST00000649888.1:n.214+2784C>T

Variant summary

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

The ENST00000649888.1(ENSG00000285698):​n.214+2784C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,054 control chromosomes in the GnomAD database, including 17,271 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 0.46 (17271 hom., cov: 32)
• Consequence: ENSG00000285698 ENST00000649888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 13 publications found

Genes affected

ENSG00000285698 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649888.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285698	ENST00000649888.1		n.214+2784C>T		intron	N/A
	NGF-AS1	ENST00000793538.1		n.228-573G>A		intron	N/A
	NGF-AS1	ENST00000793539.1		n.67+365G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69961 AN: 151938 Hom.: 17240 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.461 AC: 70038 AN: 152054 Hom.: 17271 Cov.: 32 AF XY: 0.462 AC XY: 34342 AN XY: 74306

African (AFR) AF: 0.638 AC: 26473 AN: 41488

American (AMR) AF: 0.448 AC: 6855 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2773 AN: 5154

South Asian (SAS) AF: 0.538 AC: 2593 AN: 4824

European-Finnish (FIN) AF: 0.309 AC: 3264 AN: 10564

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25122 AN: 67942

Other (OTH) AF: 0.450 AC: 951 AN: 2112

Alfa AF: 0.409 Hom.: 22796

Bravo AF: 0.477

Asia WGS AF: 0.538 AC: 1870 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	5.3
DANN	Benign	0.71
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7523086; hg19: chr1-115823387;