chr3-115704382-C-T

Variant summary

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

The NM_002045.4(GAP43):​c.629-16412C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,706 control chromosomes in the GnomAD database, including 15,604 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 0.44 ( 15604 hom., cov: 32)

Consequence

GAP43
NM_002045.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.844
Variant links:
Genes affected
GAP43 (HGNC:4140): (growth associated protein 43) The protein encoded by this gene has been termed a 'growth' or 'plasticity' protein because it is expressed at high levels in neuronal growth cones during development and axonal regeneration. This protein is considered a crucial component of an effective regenerative response in the nervous system. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GAP43NM_002045.4 linkuse as main transcriptc.629-16412C>T intron_variant ENST00000305124.11
GAP43NM_001130064.2 linkuse as main transcriptc.737-16412C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GAP43ENST00000305124.11 linkuse as main transcriptc.629-16412C>T intron_variant 1 NM_002045.4 P1P17677-1
GAP43ENST00000393780.3 linkuse as main transcriptc.737-16412C>T intron_variant 1 P17677-2

Frequencies

GnomAD3 genomes
AF:
0.444
AC:
67380
AN:
151590
Hom.:
15564
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.562
Gnomad AMI
AF:
0.414
Gnomad AMR
AF:
0.445
Gnomad ASJ
AF:
0.364
Gnomad EAS
AF:
0.267
Gnomad SAS
AF:
0.480
Gnomad FIN
AF:
0.382
Gnomad MID
AF:
0.392
Gnomad NFE
AF:
0.400
Gnomad OTH
AF:
0.404
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.445
AC:
67483
AN:
151706
Hom.:
15604
Cov.:
32
AF XY:
0.445
AC XY:
32973
AN XY:
74126
show subpopulations
Gnomad4 AFR
AF:
0.562
Gnomad4 AMR
AF:
0.446
Gnomad4 ASJ
AF:
0.364
Gnomad4 EAS
AF:
0.267
Gnomad4 SAS
AF:
0.480
Gnomad4 FIN
AF:
0.382
Gnomad4 NFE
AF:
0.400
Gnomad4 OTH
AF:
0.402
Alfa
AF:
0.356
Hom.:
1769
Bravo
AF:
0.449
Asia WGS
AF:
0.401
AC:
1392
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
3.6
DANN
Benign
0.50

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: rs283393; hg19: chr3-115423229; API