rs12760036

chr1-115305829-A-C

Variant summary

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

The NM_002506.3(NGF):c.-136-12079T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,234 control chromosomes in the GnomAD database, including 1,052 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 0.093 (1052 hom., cov: 33)
• Consequence: NGF NM_002506.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.58

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 = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NGF	NM_002506.3	c.-136-12079T>G		intron_variant		ENST00000369512.3
NGF-AS1	NR_157569.1	n.207+22589A>C		intron_variant, non_coding_transcript_variant
NGF	XM_006710663.4	c.-12-19022T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NGF	ENST00000369512.3	c.-136-12079T>G		intron_variant		1	NM_002506.3	P1
NGF-AS1	ENST00000425449.1	n.207+22589A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 14064 AN: 152116 Hom.: 1045 Cov.: 33

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0925 AC: 14086 AN: 152234 Hom.: 1052 Cov.: 33 AF XY: 0.0995 AC XY: 7403 AN XY: 74418

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.0954

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0825

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0999 Hom.: 697

Bravo AF: 0.0957

Asia WGS AF: 0.254 AC: 881 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	7.2
Dann	Benign	0.52

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: rs12760036; hg19: chr1-115848450;