rs10517368

Variant names:

• chr4-56081414-A-C
• rs10517368
• NM_001393381.1:c.-336+32115A>C

Your query was ambiguous. Multiple possible variants found:

• chr4-56081414-A-C
• chr4-56081414-A-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.-336+32115A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0287 in 152,204 control chromosomes in the GnomAD database, including 127 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 0.029 (127 hom., cov: 33)
• Consequence: CRACD NM_001393381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0735 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.-336+32115A>C		intron	N/A	NP_001380310.1	Q6ZU35
	CRACD	NM_001393383.1		c.-227+32115A>C		intron	N/A	NP_001380312.1
	CRACD	NM_001393384.1		c.-374+32115A>C		intron	N/A	NP_001380313.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRACD	ENST00000682029.1	MANE Select	c.-336+32115A>C		intron	N/A	ENSP00000507165.1	Q6ZU35
	CRACD	ENST00000646253.2		c.-165+31402A>C		intron	N/A	ENSP00000495373.2	A0A2R8Y6P1
	CRACD	ENST00000636006.1	TSL:5	c.-336+31402A>C		intron	N/A	ENSP00000490902.1	A0A1B0GWF1

Frequencies

GnomAD3 genomes AF: 0.0285 AC: 4333 AN: 152086 Hom.: 120 Cov.: 33

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.0743

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.0243

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0156

Gnomad OTH AF: 0.0364

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

GnomAD4 genome AF: 0.0287 AC: 4364 AN: 152204 Hom.: 127 Cov.: 33 AF XY: 0.0303 AC XY: 2255 AN XY: 74420

African (AFR) AF: 0.0242 AC: 1004 AN: 41522

American (AMR) AF: 0.0771 AC: 1180 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3470

East Asian (EAS) AF: 0.0745 AC: 386 AN: 5184

South Asian (SAS) AF: 0.0704 AC: 339 AN: 4814

European-Finnish (FIN) AF: 0.0243 AC: 258 AN: 10600

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0156 AC: 1062 AN: 68000

Other (OTH) AF: 0.0403 AC: 85 AN: 2110

Alfa AF: 0.0182 Hom.: 59

Bravo AF: 0.0332

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.74
PhyloP100		-0.0030

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10517368; hg19: chr4-56947580;