4-5885713-A-T

Position:

• chr4-5885713-A-T

Variant summary

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

The NM_001014809.3(CRMP1):​c.381+6876T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,868 control chromosomes in the GnomAD database, including 14,442 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 0.39 (14442 hom., cov: 32)
• Consequence: CRMP1 NM_001014809.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

CRMP1 (HGNC:2365): (collapsin response mediator protein 1) This gene encodes a member of a family of cytosolic phosphoproteins expressed exclusively in the nervous system. The encoded protein is thought to be a part of the semaphorin signal transduction pathway implicated in semaphorin-induced growth cone collapse during neural development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRMP1	NM_001014809.3	c.381+6876T>A		intron_variant		ENST00000324989.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRMP1	ENST00000324989.12	c.381+6876T>A		intron_variant		1	NM_001014809.3

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59404 AN: 151750 Hom.: 14449 Cov.: 32

Gnomad AFR AF: 0.0981

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.391 AC: 59391 AN: 151868 Hom.: 14442 Cov.: 32 AF XY: 0.393 AC XY: 29188 AN XY: 74208

Gnomad4 AFR AF: 0.0978

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.399

Alfa AF: 0.328 Hom.: 1094

Bravo AF: 0.370

Asia WGS AF: 0.566 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.51

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: rs3774895; hg19: chr4-5887440;