Variant 2-97658986-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_005735.4(ACTR1B):c.333G>A(p.Thr111Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00547 in 1,614,090 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0053 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0055 ( 37 hom. )

Consequence

ACTR1B
NM_005735.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.469

Variant links:

Genes affected

ACTR1B (HGNC:168): (actin related protein 1B) This gene encodes a 42.3 kD subunit of dynactin, a macromolecular complex consisting of 10 subunits ranging in size from 22 to 150 kD. Dynactin binds to both microtubules and cytoplasmic dynein and is involved in a diverse array of cellular functions, including ER-to-Golgi transport, the centripetal movement of lysosomes and endosomes, spindle formation, chromosome movement, nuclear positioning, and axonogenesis. This subunit, like ACTR1A, is an actin-related protein. These two proteins, which are of equal length and share 90% amino acid identity, are present in a constant ratio of approximately 1:15 in the dynactin complex. [provided by RefSeq, Aug 2008]

ACTR1B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 2-97658986-C-T is Benign according to our data. Variant chr2-97658986-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651171.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACTR1B	NM_005735.4 link	c.333G>A	p.Thr111Thr	synonymous_variant	5/11	ENST00000289228.7	NP_005726.1	P42025
ACTR1B	XM_017003116.2 link	c.201G>A	p.Thr67Thr	synonymous_variant	5/11		XP_016858605.1
ACTR1B	XM_005263854.6 link	c.111G>A	p.Thr37Thr	synonymous_variant	4/10		XP_005263911.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ACTR1B	ENST00000289228.7 link	c.333G>A	p.Thr111Thr	synonymous_variant	5/11	1	NM_005735.4	ENSP00000289228.5	P42025
ACTR1B	ENST00000451664.1 link	n.359G>A		non_coding_transcript_exon_variant	5/7	5
ACTR1B	ENST00000460427.2 link	n.558G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.00532

AC:

810

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00386

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00380

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.0171

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00551

Gnomad OTH

AF:

0.00479

GnomAD3 exomes

AF:

0.00495

AC:

1244

AN:

251366

Hom.:

AF XY:

0.00492

AC XY:

669

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.00394

Gnomad AMR exome

AF:

0.00254

Gnomad ASJ exome

AF:

0.00129

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00350

Gnomad FIN exome

AF:

0.0137

Gnomad NFE exome

AF:

0.00560

Gnomad OTH exome

AF:

0.00635

GnomAD4 exome

AF:

0.00549

AC:

8020

AN:

1461818

Hom.:

Cov.:

AF XY:

0.00531

AC XY:

3862

AN XY:

727210

show subpopulations

Gnomad4 AFR exome

AF:

0.00442

Gnomad4 AMR exome

AF:

0.00253

Gnomad4 ASJ exome

AF:

0.00107

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00381

Gnomad4 FIN exome

AF:

0.0135

Gnomad4 NFE exome

AF:

0.00564

Gnomad4 OTH exome

AF:

0.00649

GnomAD4 genome

AF:

0.00532

AC:

810

AN:

152272

Hom.:

Cov.:

AF XY:

0.00594

AC XY:

442

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.00385

Gnomad4 AMR

AF:

0.00379

Gnomad4 ASJ

AF:

0.00230

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00332

Gnomad4 FIN

AF:

0.0171

Gnomad4 NFE

AF:

0.00551

Gnomad4 OTH

AF:

0.00474

Alfa

AF:

0.00485

Hom.:

Bravo

AF:

0.00392

EpiCase

AF:

0.00507

EpiControl

AF:

0.00486

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

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

ACTR1B: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

DANN

Benign

0.66

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.29

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.29

Position offset: -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