rs9817055

Variant names:

• chr3-33528835-G-A
• rs9817055
• NM_001365631.1:c.3787+6398C>T

Variant summary

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

The NM_001365631.1(CLASP2):​c.3787+6398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,784 control chromosomes in the GnomAD database, including 8,914 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 0.33 (8914 hom., cov: 31)
• Consequence: CLASP2 NM_001365631.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 5 publications found

Genes affected

CLASP2 (HGNC:17078): (cytoplasmic linker associated protein 2) Enables cytoskeletal protein binding activity; dystroglycan binding activity; and protein tyrosine kinase binding activity. Involved in several processes, including microtubule cytoskeleton organization; positive regulation of extracellular matrix organization; and regulation of supramolecular fiber organization. Located in several cellular components, including basal cortex; cortical microtubule plus-end; and ruffle membrane. Colocalizes with focal adhesion; kinetochore; and microtubule cytoskeleton. [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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365631.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLASP2	NM_001365631.1	MANE Select	c.3787+6398C>T		intron	N/A	NP_001352560.1
	CLASP2	NM_001365628.1		c.3874+6398C>T		intron	N/A	NP_001352557.1
	CLASP2	NM_001365629.1		c.3871+6398C>T		intron	N/A	NP_001352558.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLASP2	ENST00000682230.1	MANE Select	c.3787+6398C>T		intron	N/A	ENSP00000507498.1
	CLASP2	ENST00000468888.6	TSL:5	c.3811+6398C>T		intron	N/A	ENSP00000419974.2
	CLASP2	ENST00000399362.8	TSL:5	c.3808+6398C>T		intron	N/A	ENSP00000382297.4

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50629 AN: 151666 Hom.: 8883 Cov.: 31

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.334 AC: 50708 AN: 151784 Hom.: 8914 Cov.: 31 AF XY: 0.339 AC XY: 25154 AN XY: 74172

African (AFR) AF: 0.398 AC: 16464 AN: 41394

American (AMR) AF: 0.458 AC: 6970 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3466

East Asian (EAS) AF: 0.368 AC: 1899 AN: 5154

South Asian (SAS) AF: 0.323 AC: 1554 AN: 4806

European-Finnish (FIN) AF: 0.315 AC: 3318 AN: 10536

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.276 AC: 18730 AN: 67906

Other (OTH) AF: 0.335 AC: 702 AN: 2096

Alfa AF: 0.296 Hom.: 16690

Bravo AF: 0.349

Asia WGS AF: 0.379 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.36
PhyloP100		-2.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs9817055; hg19: chr3-33570327;