rs707859

chr6-17497260-T-Achr6-17497260-T-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAP2	NM_006366.3	c.301-9909T>A		intron_variant		ENST00000229922.7
CAP2	NM_001363533.2	c.300+34187T>A		intron_variant
CAP2	NM_001363534.2	c.223-9909T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAP2	ENST00000229922.7	c.301-9909T>A		intron_variant		1	NM_006366.3	P1

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

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.724

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
Cadd	Benign	3.6
Dann	Benign	0.89

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: rs707859; hg19: chr6-17497491;