1-115289162-C-T

Variant summary

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

The NM_002506.3(NGF):c.-12-2355G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 152,174 control chromosomes in the GnomAD database, including 664 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 0.077 (664 hom., cov: 32)
• Consequence: NGF NM_002506.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

Genes affected

NGF (HGNC:7808): (nerve growth factor) This gene is a member of the NGF-beta family and encodes a secreted protein which homodimerizes and is incorporated into a larger complex. This protein has nerve growth stimulating activity and the complex is involved in the regulation of growth and the differentiation of sympathetic and certain sensory neurons. Mutations in this gene have been associated with hereditary sensory and autonomic neuropathy, type 5 (HSAN5), and dysregulation of this gene's expression is associated with allergic rhinitis. [provided by RefSeq, Jul 2008]

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NGF	NM_002506.3	c.-12-2355G>A		intron_variant		ENST00000369512.3
NGF-AS1	NR_157569.1	n.207+5922C>T		intron_variant, non_coding_transcript_variant
NGF	XM_006710663.4	c.-12-2355G>A		intron_variant
NGF	XM_011541518.3	c.154-2355G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NGF	ENST00000369512.3	c.-12-2355G>A		intron_variant		1	NM_002506.3	P1
NGF-AS1	ENST00000425449.1	n.207+5922C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11732 AN: 152056 Hom.: 659 Cov.: 32

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.0772 AC: 11754 AN: 152174 Hom.: 664 Cov.: 32 AF XY: 0.0807 AC XY: 6004 AN XY: 74392

Gnomad4 AFR AF: 0.0369

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0988

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.0758

Gnomad4 NFE AF: 0.0646

Gnomad4 OTH AF: 0.0874

Alfa AF: 0.0655 Hom.: 306

Bravo AF: 0.0793

Asia WGS AF: 0.246 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.4
Dann	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2268793; hg19: chr1-115831783;