3-115704382-C-T

Variant names:

• chr3-115704382-C-T
• rs283393
• NM_002045.4:c.629-16412C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

ENSG00000289153 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GAP43	NM_002045.4	c.629-16412C>T		intron_variant	Intron 2 of 2	ENST00000305124.11	NP_002036.1
GAP43	NM_001130064.2	c.737-16412C>T		intron_variant	Intron 3 of 3		NP_001123536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAP43	ENST00000305124.11	c.629-16412C>T		intron_variant	Intron 2 of 2	1	NM_002045.4	ENSP00000305010.7
GAP43	ENST00000393780.3	c.737-16412C>T		intron_variant	Intron 3 of 3	1		ENSP00000377372.3
ENSG00000289153	ENST00000750609.1	n.209-11132G>A		intron_variant	Intron 1 of 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

African (AFR) AF: 0.562 AC: 23292 AN: 41414

American (AMR) AF: 0.446 AC: 6774 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1259 AN: 3462

East Asian (EAS) AF: 0.267 AC: 1378 AN: 5162

South Asian (SAS) AF: 0.480 AC: 2310 AN: 4812

European-Finnish (FIN) AF: 0.382 AC: 4020 AN: 10514

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27117 AN: 67836

Other (OTH) AF: 0.402 AC: 844 AN: 2098

Alfa AF: 0.384 Hom.: 3937

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
PhyloP100		0.84
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: rs283393; hg19: chr3-115423229;