Variant 7-5527651-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_001101.5(ACTB):c.*96_*97insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0302 in 145,440 control chromosomes in the GnomAD database, including 70 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.030 ( 70 hom., cov: 31)

Exomes 𝑓: 0.036 ( 748 hom. )

Failed GnomAD Quality Control

Consequence

ACTB
NM_001101.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0270

Variant links:

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]

ACTB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-5527651-C-CA is Benign according to our data. Variant chr7-5527651-C-CA is described in ClinVar as [Likely_benign]. Clinvar id is 1213113.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0302 (4391/145440) while in subpopulation NFE AF= 0.0328 (2161/65922). AF 95% confidence interval is 0.0316. There are 70 homozygotes in gnomad4. There are 2017 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd4 at 4391 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACTB	NM_001101.5 linkuse as main transcript	c.96_97insT		3_prime_UTR_variant	6/6	ENST00000646664.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACTB	ENST00000646664.1 linkuse as main transcript	c.96_97insT		3_prime_UTR_variant	6/6		NM_001101.5	P1

Frequencies

GnomAD3 genomes

AF:

0.0302

AC:

4389

AN:

145374

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0307

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0278

Gnomad ASJ

AF:

0.0601

Gnomad EAS

AF:

0.0117

Gnomad SAS

AF:

0.0241

Gnomad FIN

AF:

0.0110

Gnomad MID

AF:

0.0691

Gnomad NFE

AF:

0.0328

Gnomad OTH

AF:

0.0343

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0365

AC:

43044

AN:

1180568

Hom.:

748

Cov.:

AF XY:

0.0362

AC XY:

21358

AN XY:

589430

show subpopulations

Gnomad4 AFR exome

AF:

0.0384

Gnomad4 AMR exome

AF:

0.0212

Gnomad4 ASJ exome

AF:

0.0662

Gnomad4 EAS exome

AF:

0.0147

Gnomad4 SAS exome

AF:

0.0333

Gnomad4 FIN exome

AF:

0.0145

Gnomad4 NFE exome

AF:

0.0384

Gnomad4 OTH exome

AF:

0.0353

GnomAD4 genome

AF:

0.0302

AC:

4391

AN:

145440

Hom.:

Cov.:

AF XY:

0.0285

AC XY:

2017

AN XY:

70664

show subpopulations

Gnomad4 AFR

AF:

0.0307

Gnomad4 AMR

AF:

0.0278

Gnomad4 ASJ

AF:

0.0601

Gnomad4 EAS

AF:

0.0118

Gnomad4 SAS

AF:

0.0240

Gnomad4 FIN

AF:

0.0110

Gnomad4 NFE

AF:

0.0328

Gnomad4 OTH

AF:

0.0341

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over