rs776352029

Variant names:

• chr4-56313293-C-G
• rs776352029
• NM_001393381.1:c.451C>G

Your query was ambiguous. Multiple possible variants found:

• chr4-56313293-C-G
• chr4-56313293-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001393381.1(CRACD):​c.451C>G​(p.Arg151Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R151H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CRACD NM_001393381.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.16
• Publications: 1 publications found

Genes affected

CRACD (HGNC:29219): (capping protein inhibiting regulator of actin dynamics) Involved in negative regulation of barbed-end actin filament capping. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393381.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRACD	NM_001393381.1	MANE Select	c.451C>G	p.Arg151Gly	missense	Exon 7 of 11	NP_001380310.1	Q6ZU35
	CRACD	NM_001393382.1		c.451C>G	p.Arg151Gly	missense	Exon 6 of 10	NP_001380311.1	Q6ZU35
	CRACD	NM_020722.2		c.451C>G	p.Arg151Gly	missense	Exon 7 of 11	NP_065773.1	Q6ZU35

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRACD	ENST00000682029.1	MANE Select	c.451C>G	p.Arg151Gly	missense	Exon 7 of 11	ENSP00000507165.1	Q6ZU35
	CRACD	ENST00000541073.5	TSL:1	c.430C>G	p.Arg144Gly	missense	Exon 6 of 10	ENSP00000444006.1	F5H1N7
	CRACD	ENST00000646253.2		c.706C>G	p.Arg236Gly	missense	Exon 8 of 12	ENSP00000495373.2	A0A2R8Y6P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.41
BayesDel_addAF	Uncertain	0.047	T
BayesDel_noAF	Benign	-0.17
CADD	Uncertain	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.11	T
Eigen	Uncertain	0.56
Eigen_PC	Uncertain	0.51
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.87	D
M_CAP	Benign	0.055	D
MetaRNN	Uncertain	0.48	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.7	M
PhyloP100		3.2
PrimateAI	Benign	0.38	T
PROVEAN	Uncertain	-3.9	D
REVEL	Benign	0.28
Sift	Benign	0.13	T
Sift4G	Benign	0.14	T
Polyphen		1.0	D
Vest4		0.75
MutPred		0.54		Loss of MoRF binding (P = 0.0126)
MVP		0.37
MPC		1.1
ClinPred		0.97	D
GERP RS		4.6
Varity_R		0.32
gMVP		0.47
Mutation Taster		=72/28	polymorphism

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: rs776352029; hg19: chr4-57179459;