3-115704382-C-T

Position:

• chr3-115704382-C-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.844

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]

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 (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
GAP43	NM_002045.4	c.629-16412C>T		intron_variant		ENST00000305124.11
GAP43	NM_001130064.2	c.737-16412C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAP43	ENST00000305124.11	c.629-16412C>T		intron_variant		1	NM_002045.4	P1
GAP43	ENST00000393780.3	c.737-16412C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67380 AN: 151590 Hom.: 15564 Cov.: 32

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

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

Other links and lift over

dbSNP: rs283393; hg19: chr3-115423229;