rs7667

Variant names:

• chr1-19392330-G-A
• rs7667
• NM_004930.5:c.94-6704C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-19392330-G-A
• chr1-19392330-G-C
• chr1-19392330-G-T

Variant summary

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

The NM_004930.5(CAPZB):​c.94-6704C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,588 control chromosomes in the GnomAD database, including 7,945 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 0.32 (7945 hom., cov: 28)
• Consequence: CAPZB NM_004930.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.708
• Publications: 12 publications found

Genes affected

CAPZB (HGNC:1491): (capping actin protein of muscle Z-line subunit beta) This gene encodes the beta subunit of the barbed-end actin binding protein, which belongs to the F-actin capping protein family. The capping protein is a heterodimeric actin capping protein that blocks actin filament assembly and disassembly at the fast growing (barbed) filament ends and functions in regulating actin filament dynamics as well as in stabilizing actin filament lengths in muscle and nonmuscle cells. A pseudogene of this gene is located on the long arm of chromosome 2. Multiple alternatively spliced transcript variants encoding different isoforms have been found.[provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.337 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004930.5. 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
	CAPZB	NM_004930.5	MANE Select	c.94-6704C>T		intron	N/A	NP_004921.1
	CAPZB	NM_001282162.2		c.181-6704C>T		intron	N/A	NP_001269091.1
	CAPZB	NM_001206540.3		c.94-6704C>T		intron	N/A	NP_001193469.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAPZB	ENST00000264202.8	TSL:1 MANE Select	c.94-6704C>T		intron	N/A	ENSP00000264202.7
	CAPZB	ENST00000375144.6	TSL:1	c.94-6704C>T		intron	N/A	ENSP00000364286.2
	CAPZB	ENST00000433834.5	TSL:2	c.181-6704C>T		intron	N/A	ENSP00000401010.1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48828 AN: 151468 Hom.: 7935 Cov.: 28

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.322 AC: 48861 AN: 151588 Hom.: 7945 Cov.: 28 AF XY: 0.320 AC XY: 23720 AN XY: 74050

African (AFR) AF: 0.293 AC: 12086 AN: 41292

American (AMR) AF: 0.326 AC: 4967 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3468

East Asian (EAS) AF: 0.350 AC: 1802 AN: 5144

South Asian (SAS) AF: 0.312 AC: 1497 AN: 4798

European-Finnish (FIN) AF: 0.324 AC: 3403 AN: 10502

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22800 AN: 67862

Other (OTH) AF: 0.318 AC: 668 AN: 2102

Alfa AF: 0.334 Hom.: 14478

Bravo AF: 0.324

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.71
PhyloP100		0.71
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: rs7667; hg19: chr1-19718824;