chr2-85395194-T-C

Variant names:

• chr2-85395194-T-C
• rs11690650
• NM_001747.4:c.982-236A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001747.4. 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
	CAPG	NM_001747.4	MANE Select	c.982-236A>G		intron	N/A	NP_001738.2	P40121-1
	CAPG	NM_001256139.2		c.982-236A>G		intron	N/A	NP_001243068.1	P40121-1
	CAPG	NM_001320732.2		c.982-236A>G		intron	N/A	NP_001307661.1	P40121-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPG	ENST00000263867.9	TSL:1 MANE Select	c.982-236A>G		intron	N/A	ENSP00000263867.4	P40121-1
	CAPG	ENST00000409724.5	TSL:1	c.982-236A>G		intron	N/A	ENSP00000386965.1	P40121-1
	CAPG	ENST00000409921.5	TSL:1	c.937-236A>G		intron	N/A	ENSP00000387063.1	P40121-2

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

African (AFR) AF: 0.296 AC: 12273 AN: 41440

American (AMR) AF: 0.141 AC: 2153 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3472

East Asian (EAS) AF: 0.100 AC: 518 AN: 5156

South Asian (SAS) AF: 0.259 AC: 1245 AN: 4808

European-Finnish (FIN) AF: 0.196 AC: 2074 AN: 10576

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15785 AN: 67960

Other (OTH) AF: 0.185 AC: 390 AN: 2110

Alfa AF: 0.224 Hom.: 12246

Bravo AF: 0.223

Asia WGS AF: 0.198 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.083
DANN	Benign	0.54
PhyloP100		-0.55
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: rs11690650; hg19: chr2-85622317;