chr3-115666835-A-G

Variant names:

• chr3-115666835-A-G
• rs9860828
• NM_002045.4:c.31-9178A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002045.4(GAP43):​c.31-9178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,946 control chromosomes in the GnomAD database, including 19,824 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 0.49 (19824 hom., cov: 31)
• Consequence: GAP43 NM_002045.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAP43	NM_002045.4	c.31-9178A>G		intron_variant	Intron 1 of 2	ENST00000305124.11	NP_002036.1
GAP43	NM_001130064.2	c.138+2919A>G		intron_variant	Intron 2 of 3		NP_001123536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAP43	ENST00000305124.11	c.31-9178A>G		intron_variant	Intron 1 of 2	1	NM_002045.4	ENSP00000305010.7
GAP43	ENST00000393780.3	c.138+2919A>G		intron_variant	Intron 2 of 3	1		ENSP00000377372.3

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73978 AN: 151828 Hom.: 19768 Cov.: 31

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.488 AC: 74093 AN: 151946 Hom.: 19824 Cov.: 31 AF XY: 0.491 AC XY: 36466 AN XY: 74254

African (AFR) AF: 0.710 AC: 29458 AN: 41508

American (AMR) AF: 0.509 AC: 7755 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1345 AN: 3464

East Asian (EAS) AF: 0.609 AC: 3138 AN: 5150

South Asian (SAS) AF: 0.422 AC: 2033 AN: 4812

European-Finnish (FIN) AF: 0.427 AC: 4504 AN: 10544

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24470 AN: 67900

Other (OTH) AF: 0.491 AC: 1037 AN: 2114

Alfa AF: 0.427 Hom.: 23534

Bravo AF: 0.504

Asia WGS AF: 0.529 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.056
DANN	Benign	0.42
PhyloP100		-2.8
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: rs9860828; hg19: chr3-115385682;