rs2932529

Variant names:

• chr1-112650742-G-A
• rs2932529
• NM_006135.3:c.155+1273G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-112650742-G-A
• chr1-112650742-G-C

Variant summary

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

The NM_006135.3(CAPZA1):​c.155+1273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,252 control chromosomes in the GnomAD database, including 49,519 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 0.80 (49519 hom., cov: 33)
• Consequence: CAPZA1 NM_006135.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 5 publications found

Genes affected

CAPZA1 (HGNC:1488): (capping actin protein of muscle Z-line subunit alpha 1) CAPZA1 is a member of the F-actin capping protein alpha subunit family. This gene encodes the alpha subunit of the barbed-end actin binding protein. The protein regulates growth of the actin filament by capping the barbed end of growing actin filaments. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006135.3. 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
	CAPZA1	NM_006135.3	MANE Select	c.155+1273G>A		intron	N/A	NP_006126.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPZA1	ENST00000263168.4	TSL:1 MANE Select	c.155+1273G>A		intron	N/A	ENSP00000263168.3
	CAPZA1	ENST00000904626.1		c.155+1273G>A		intron	N/A	ENSP00000574685.1
	CAPZA1	ENST00000917728.1		c.155+1273G>A		intron	N/A	ENSP00000587787.1

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122190 AN: 152134 Hom.: 49460 Cov.: 33

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.803 AC: 122307 AN: 152252 Hom.: 49519 Cov.: 33 AF XY: 0.808 AC XY: 60171 AN XY: 74442

African (AFR) AF: 0.872 AC: 36229 AN: 41560

American (AMR) AF: 0.850 AC: 13013 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2726 AN: 3472

East Asian (EAS) AF: 0.911 AC: 4717 AN: 5180

South Asian (SAS) AF: 0.900 AC: 4341 AN: 4822

European-Finnish (FIN) AF: 0.776 AC: 8234 AN: 10608

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50429 AN: 67992

Other (OTH) AF: 0.809 AC: 1707 AN: 2110

Alfa AF: 0.772 Hom.: 5913

Bravo AF: 0.814

Asia WGS AF: 0.904 AC: 3143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		0.045
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: rs2932529; hg19: chr1-113193364; COSMIC: COSV54144728; COSMIC: COSV54144728;