rs707859

Variant names:

• chr6-17497260-T-A
• rs707859
• NM_006366.3:c.301-9909T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-17497260-T-A
• chr6-17497260-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_006366.3(CAP2):​c.301-9909T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,130 control chromosomes in the GnomAD database, including 41,906 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 0.74 (41906 hom., cov: 32)
• Consequence: CAP2 NM_006366.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 1 publications found

Genes affected

CAP2 (HGNC:20039): (cyclase associated actin cytoskeleton regulatory protein 2) This gene was identified by its similarity to the gene for human adenylyl cyclase-associated protein. The function of the protein encoded by this gene is unknown. However, the protein appears to be able to interact with adenylyl cyclase-associated protein and actin. [provided by RefSeq, Jul 2008]

CAP2 Gene-Disease associations (from GenCC):

• cardiomyopathy, dilated, 2I

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics
• familial isolated dilated cardiomyopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006366.3. 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
	CAP2	NM_006366.3	MANE Select	c.301-9909T>A		intron	N/A	NP_006357.1	P40123-1
	CAP2	NM_001363534.2		c.223-9909T>A		intron	N/A	NP_001350463.1	E9PDI2
	CAP2	NM_001363533.2		c.300+34187T>A		intron	N/A	NP_001350462.1	B7Z385

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAP2	ENST00000229922.7	TSL:1 MANE Select	c.301-9909T>A		intron	N/A	ENSP00000229922.2	P40123-1
	CAP2	ENST00000479291.5	TSL:1	n.223-9909T>A		intron	N/A	ENSP00000420615.1	F8WDB9
	CAP2	ENST00000857692.1		c.301-9909T>A		intron	N/A	ENSP00000527751.1

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112584 AN: 152012 Hom.: 41856 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.741 AC: 112695 AN: 152130 Hom.: 41906 Cov.: 32 AF XY: 0.746 AC XY: 55484 AN XY: 74386

African (AFR) AF: 0.769 AC: 31944 AN: 41514

American (AMR) AF: 0.744 AC: 11379 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2310 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3832 AN: 5168

South Asian (SAS) AF: 0.716 AC: 3440 AN: 4804

European-Finnish (FIN) AF: 0.798 AC: 8441 AN: 10584

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48896 AN: 67990

Other (OTH) AF: 0.724 AC: 1529 AN: 2112

Alfa AF: 0.739 Hom.: 5184

Bravo AF: 0.735

Asia WGS AF: 0.743 AC: 2583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	3.6
DANN	Benign	0.89
PhyloP100		0.31
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: rs707859; hg19: chr6-17497491;