rs17033692

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002506.3(NGF):​c.-137+10975A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0934 in 152,288 control chromosomes in the GnomAD database, including 802 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 ( 802 hom., cov: 33)

Consequence

NGF
NM_002506.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.324
Variant links:
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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NGFNM_002506.3 linkc.-137+10975A>G intron_variant ENST00000369512.3 NP_002497.2 P01138
NGFXM_006710663.4 linkc.-13+10975A>G intron_variant XP_006710726.1 P01138
NGF-AS1NR_157569.1 linkn.208-38441T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NGFENST00000369512.3 linkc.-137+10975A>G intron_variant 1 NM_002506.3 ENSP00000358525.2 P01138

Frequencies

GnomAD3 genomes
AF:
0.0934
AC:
14206
AN:
152170
Hom.:
794
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0846
Gnomad AMI
AF:
0.0844
Gnomad AMR
AF:
0.150
Gnomad ASJ
AF:
0.0991
Gnomad EAS
AF:
0.254
Gnomad SAS
AF:
0.125
Gnomad FIN
AF:
0.107
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.0692
Gnomad OTH
AF:
0.0929
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0934
AC:
14227
AN:
152288
Hom.:
802
Cov.:
33
AF XY:
0.0976
AC XY:
7267
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0846
Gnomad4 AMR
AF:
0.151
Gnomad4 ASJ
AF:
0.0991
Gnomad4 EAS
AF:
0.254
Gnomad4 SAS
AF:
0.124
Gnomad4 FIN
AF:
0.107
Gnomad4 NFE
AF:
0.0692
Gnomad4 OTH
AF:
0.0943
Alfa
AF:
0.0763
Hom.:
995
Bravo
AF:
0.0989
Asia WGS
AF:
0.181
AC:
627
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
6.6
DANN
Benign
0.36

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17033692; hg19: chr1-115869850; API