rs984576

chr4-5850411-G-Achr4-5850411-G-Cchr4-5850411-G-T

Variant summary

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

The NM_001014809.3(CRMP1):c.883-939C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,006 control chromosomes in the GnomAD database, including 22,028 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 0.51 (22028 hom., cov: 32)
• Consequence: CRMP1 NM_001014809.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRMP1	NM_001014809.3	c.883-939C>T		intron_variant		ENST00000324989.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRMP1	ENST00000324989.12	c.883-939C>T		intron_variant		1	NM_001014809.3

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78048 AN: 151888 Hom.: 22025 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.514 AC: 78072 AN: 152006 Hom.: 22028 Cov.: 32 AF XY: 0.518 AC XY: 38452 AN XY: 74278

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.520

Alfa AF: 0.584 Hom.: 35391

Bravo AF: 0.485

Asia WGS AF: 0.711 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.23
Dann	Benign	0.23

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: rs984576; hg19: chr4-5852138;