ENST00000793538.1:n.374G>C

Variant names:

• chr1-115281571-G-C
• rs7523831
• ENST00000793538.1:n.374G>C

Variant summary

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

The ENST00000793538.1(NGF-AS1):​n.374G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,048 control chromosomes in the GnomAD database, including 18,645 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 0.47 (18645 hom., cov: 32)
• Consequence: NGF-AS1 ENST00000793538.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 5 publications found

Genes affected

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

ENSG00000285698 (HGNC:):

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 = 0.68 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

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
	NGF-AS1	ENST00000793538.1		n.374G>C		non_coding_transcript_exon	Exon 4 of 5
	NGF-AS1	ENST00000793539.1		n.126G>C		non_coding_transcript_exon	Exon 2 of 3
	NGF-AS1	ENST00000793540.1		n.93G>C		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72013 AN: 151930 Hom.: 18619 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.474 AC: 72086 AN: 152048 Hom.: 18645 Cov.: 32 AF XY: 0.475 AC XY: 35265 AN XY: 74308

African (AFR) AF: 0.686 AC: 28468 AN: 41474

American (AMR) AF: 0.451 AC: 6896 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3468

East Asian (EAS) AF: 0.534 AC: 2755 AN: 5164

South Asian (SAS) AF: 0.538 AC: 2592 AN: 4814

European-Finnish (FIN) AF: 0.309 AC: 3265 AN: 10556

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25137 AN: 67978

Other (OTH) AF: 0.456 AC: 964 AN: 2114

Alfa AF: 0.240 Hom.: 454

Bravo AF: 0.496

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.76
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs7523831; hg19: chr1-115824192;