rs28167

Positions:

• chr7-116826029-T-C

Variant summary

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

The ENST00000464223.5(CAPZA2):​c.-29+14927T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 152,032 control chromosomes in the GnomAD database, including 28,518 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 0.60 (28518 hom., cov: 31)
• Consequence: CAPZA2 ENST00000464223.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

Genes affected

CAPZA2 (HGNC:1490): (capping actin protein of muscle Z-line subunit alpha 2) The protein encoded by this gene is a member of the F-actin capping protein alpha subunit family. It is the alpha subunit of the barbed-end actin binding protein Cap Z. By capping the barbed end of actin filaments, Cap Z regulates the growth of the actin filaments at the barbed end. [provided by RefSeq, Jul 2008]

LOC124901731 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901731	XR_007060489.1	n.84-9522T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPZA2	ENST00000464223.5	c.-29+14927T>C		intron_variant		1
CAPZA2	ENST00000484325.1	c.-189+14927T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91564 AN: 151914 Hom.: 28532 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.602 AC: 91578 AN: 152032 Hom.: 28518 Cov.: 31 AF XY: 0.609 AC XY: 45243 AN XY: 74298

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.610

Alfa AF: 0.617 Hom.: 8688

Bravo AF: 0.588

Asia WGS AF: 0.827 AC: 2874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs28167; hg19: chr7-116466083;