rs17030613

chr1-112648185-A-Cchr1-112648185-A-T

Variant summary

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

The NM_006135.3(CAPZA1):c.103+912A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,952 control chromosomes in the GnomAD database, including 3,780 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 0.20 (3780 hom., cov: 31)
• Consequence: CAPZA1 NM_006135.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAPZA1	NM_006135.3	c.103+912A>C		intron_variant		ENST00000263168.4
CAPZA1	XM_011542225.4	c.103+912A>C		intron_variant
CAPZA1	XM_017002424.3	c.103+912A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPZA1	ENST00000263168.4	c.103+912A>C		intron_variant		1	NM_006135.3	P1
CAPZA1	ENST00000476936.5	n.129+912A>C		intron_variant, non_coding_transcript_variant		3
CAPZA1	ENST00000485542.5	n.143+912A>C		intron_variant, non_coding_transcript_variant		2
CAPZA1	ENST00000498626.1	n.156+912A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29914 AN: 151834 Hom.: 3778 Cov.: 31

Gnomad AFR AF: 0.0774

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.197 AC: 29923 AN: 151952 Hom.: 3780 Cov.: 31 AF XY: 0.209 AC XY: 15506 AN XY: 74212

Gnomad4 AFR AF: 0.0774

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.188

Alfa AF: 0.214 Hom.: 5735

Bravo AF: 0.189

Asia WGS AF: 0.318 AC: 1101 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.2
Dann	Benign	0.46

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: rs17030613; hg19: chr1-113190807;