3-115639308-G-A

Position:

• chr3-115639308-G-A

Variant summary

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

The NM_002045.4(GAP43):​c.30+15589G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,992 control chromosomes in the GnomAD database, including 17,731 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 0.48 (17731 hom., cov: 33)
• Consequence: GAP43 NM_002045.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAP43	NM_002045.4	c.30+15589G>A		intron_variant		ENST00000305124.11	NP_002036.1
GAP43	NM_001130064.2	c.-259+15589G>A		intron_variant			NP_001123536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAP43	ENST00000305124.11	c.30+15589G>A		intron_variant		1	NM_002045.4	ENSP00000305010	P1
GAP43	ENST00000393780.3	c.-259+15589G>A		intron_variant		1		ENSP00000377372

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72976 AN: 151874 Hom.: 17706 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.481 AC: 73057 AN: 151992 Hom.: 17731 Cov.: 33 AF XY: 0.486 AC XY: 36083 AN XY: 74294

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.518

Alfa AF: 0.499 Hom.: 25606

Bravo AF: 0.472

Asia WGS AF: 0.641 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.43

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: rs714697; hg19: chr3-115358155;