rs11690650

Positions:

• chr2-85395194-T-C

Variant summary

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

The NM_001747.4(CAPG):​c.982-236A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,004 control chromosomes in the GnomAD database, including 4,414 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 0.23 (4414 hom., cov: 32)
• Consequence: CAPG NM_001747.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

CAPG (HGNC:1474): (capping actin protein, gelsolin like) This gene encodes a member of the gelsolin/villin family of actin-regulatory proteins. The encoded protein reversibly blocks the barbed ends of F-actin filaments in a Ca2+ and phosphoinositide-regulated manner, but does not sever preformed actin filaments. By capping the barbed ends of actin filaments, the encoded protein contributes to the control of actin-based motility in non-muscle cells. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jan 2012]

CAPG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAPG	NM_001747.4	c.982-236A>G		intron_variant		ENST00000263867.9	NP_001738.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAPG	ENST00000263867.9	c.982-236A>G		intron_variant		1	NM_001747.4	ENSP00000263867.4

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34982 AN: 151886 Hom.: 4401 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.230 AC: 35028 AN: 152004 Hom.: 4414 Cov.: 32 AF XY: 0.226 AC XY: 16804 AN XY: 74266

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.185

Alfa AF: 0.220 Hom.: 7923

Bravo AF: 0.223

Asia WGS AF: 0.198 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.083
DANN	Benign	0.54

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: rs11690650; hg19: chr2-85622317;