4-56193641-T-C

Position:

• chr4-56193641-T-C

Variant summary

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

The NM_001393381.1(CRACD):​c.-189+14211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0332 in 152,344 control chromosomes in the GnomAD database, including 120 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 0.033 (120 hom., cov: 32)
• Consequence: CRACD NM_001393381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRACD	NM_001393381.1	c.-189+14211T>C		intron_variant		ENST00000682029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRACD	ENST00000682029.1	c.-189+14211T>C		intron_variant			NM_001393381.1	A2

Frequencies

GnomAD3 genomes AF: 0.0332 AC: 5054 AN: 152226 Hom.: 120 Cov.: 32

Gnomad AFR AF: 0.00765

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0332 AC: 5051 AN: 152344 Hom.: 120 Cov.: 32 AF XY: 0.0337 AC XY: 2510 AN XY: 74508

Gnomad4 AFR AF: 0.00762

Gnomad4 AMR AF: 0.0559

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.0590

Gnomad4 NFE AF: 0.0433

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0457 Hom.: 34

Bravo AF: 0.0322

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.0
DANN	Benign	0.86

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: rs17806720; hg19: chr4-57059807;