chr7-5527623-CA-C

Position:

• chr7-5527623-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001101.5(ACTB):​c.*124del variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.133 in 1,134,546 control chromosomes in the GnomAD database, including 104 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.080 (77 hom., cov: 30)
  • Exomes 𝑓: 0.14 (27 hom.)
• Consequence: ACTB NM_001101.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.48

Genes affected

ACTB (HGNC:132): (actin beta) This gene encodes one of six different actin proteins. Actins are highly conserved proteins that are involved in cell motility, structure, integrity, and intercellular signaling. The encoded protein is a major constituent of the contractile apparatus and one of the two nonmuscle cytoskeletal actins that are ubiquitously expressed. Mutations in this gene cause Baraitser-Winter syndrome 1, which is characterized by intellectual disability with a distinctive facial appearance in human patients. Numerous pseudogenes of this gene have been identified throughout the human genome. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-5527623-CA-C is Benign according to our data. Variant chr7-5527623-CA-C is described in ClinVar as [Benign]. Clinvar id is 1272390.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACTB	NM_001101.5	c.*124del		3_prime_UTR_variant	6/6	ENST00000646664.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACTB	ENST00000646664.1	c.*124del		3_prime_UTR_variant	6/6		NM_001101.5	P1

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 4791 AN: 59812 Hom.: 77 Cov.: 30

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.0699

Gnomad EAS AF: 0.00668

Gnomad SAS AF: 0.0264

Gnomad FIN AF: 0.0950

Gnomad MID AF: 0.0500

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0829

GnomAD4 exome AF: 0.136 AC: 145887 AN: 1074702 Hom.: 27 Cov.: 0 AF XY: 0.136 AC XY: 73275 AN XY: 538540

Gnomad4 AFR exome AF: 0.119

Gnomad4 AMR exome AF: 0.157

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.132

Gnomad4 SAS exome AF: 0.117

Gnomad4 FIN exome AF: 0.163

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.132

GnomAD4 genome AF: 0.0801 AC: 4792 AN: 59844 Hom.: 77 Cov.: 30 AF XY: 0.0787 AC XY: 2251 AN XY: 28588

Gnomad4 AFR AF: 0.0523

Gnomad4 AMR AF: 0.0640

Gnomad4 ASJ AF: 0.0699

Gnomad4 EAS AF: 0.00674

Gnomad4 SAS AF: 0.0270

Gnomad4 FIN AF: 0.0950

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0821

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs370106412; hg19: chr7-5567254;