rs629242

Variant names:

• chr4-56276871-C-T
• rs629242
• NM_001393381.1:c.-17+4379C>T

Variant summary

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

The NM_001393381.1(CRACD):​c.-17+4379C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,136 control chromosomes in the GnomAD database, including 4,927 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 0.25 (4927 hom., cov: 32)
• Consequence: CRACD NM_001393381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 15 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

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.-17+4379C>T		intron	N/A	NP_001380310.1	Q6ZU35
	CRACD	NM_001393382.1		c.-17+4379C>T		intron	N/A	NP_001380311.1	Q6ZU35
	CRACD	NM_020722.2		c.-17+4379C>T		intron	N/A	NP_065773.1	Q6ZU35

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRACD	ENST00000682029.1	MANE Select	c.-17+4379C>T		intron	N/A	ENSP00000507165.1	Q6ZU35
	CRACD	ENST00000541073.5	TSL:1	c.-60+4379C>T		intron	N/A	ENSP00000444006.1	F5H1N7
	CRACD	ENST00000646253.2		c.239+4379C>T		intron	N/A	ENSP00000495373.2	A0A2R8Y6P1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38061 AN: 152018 Hom.: 4934 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.250 AC: 38064 AN: 152136 Hom.: 4927 Cov.: 32 AF XY: 0.248 AC XY: 18463 AN XY: 74354

African (AFR) AF: 0.315 AC: 13079 AN: 41500

American (AMR) AF: 0.201 AC: 3066 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1018 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1819 AN: 5166

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4828

European-Finnish (FIN) AF: 0.225 AC: 2374 AN: 10568

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14836 AN: 67998

Other (OTH) AF: 0.266 AC: 563 AN: 2114

Alfa AF: 0.233 Hom.: 14249

Bravo AF: 0.252

Asia WGS AF: 0.312 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.51
PhyloP100		-1.4
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: rs629242; hg19: chr4-57143037;