3-115639308-G-A

Variant names:

• chr3-115639308-G-A
• rs714697
• NM_002045.4:c.30+15589G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002045.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAP43	NM_002045.4	MANE Select	c.30+15589G>A		intron	N/A	NP_002036.1
	GAP43	NM_001130064.2		c.-259+15589G>A		intron	N/A	NP_001123536.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAP43	ENST00000305124.11	TSL:1 MANE Select	c.30+15589G>A		intron	N/A	ENSP00000305010.7
	GAP43	ENST00000393780.3	TSL:1	c.-259+15589G>A		intron	N/A	ENSP00000377372.3

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

African (AFR) AF: 0.409 AC: 16984 AN: 41506

American (AMR) AF: 0.466 AC: 7104 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1801 AN: 3468

East Asian (EAS) AF: 0.576 AC: 2955 AN: 5134

South Asian (SAS) AF: 0.661 AC: 3190 AN: 4824

European-Finnish (FIN) AF: 0.533 AC: 5632 AN: 10568

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33644 AN: 67918

Other (OTH) AF: 0.518 AC: 1094 AN: 2114

Alfa AF: 0.495 Hom.: 31946

Bravo AF: 0.472

Asia WGS AF: 0.641 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.43
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs714697; hg19: chr3-115358155;