rs940261

chr7-152848266-G-A

Variant summary

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

The NM_020445.6(ACTR3B):c.952-3860G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,012 control chromosomes in the GnomAD database, including 23,889 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 0.54 (23889 hom., cov: 32)
• Consequence: ACTR3B NM_020445.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

Genes affected

ACTR3B (HGNC:17256): (actin related protein 3B) This gene encodes a member of the actin-related proteins (ARP), which form multiprotein complexes and share 35-55% amino acid identity with conventional actin. The protein encoded by this gene may have a regulatory role in the actin cytoskeleton and induce cell-shape change and motility. Pseudogenes of this gene are located on chromosomes 2, 4, 10, 16, 22 and Y. Alternative splicing results in multiple transcript variants and protein isoforms. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACTR3B	NM_020445.6	c.952-3860G>A		intron_variant		ENST00000256001.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACTR3B	ENST00000256001.13	c.952-3860G>A		intron_variant		1	NM_020445.6	P1
ACTR3B	ENST00000377776.7	c.952-6192G>A		intron_variant		1
ACTR3B	ENST00000397282.2	c.688-3860G>A		intron_variant		2
ACTR3B	ENST00000479402.1	n.4420-3860G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82286 AN: 151894 Hom.: 23875 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.542 AC: 82322 AN: 152012 Hom.: 23889 Cov.: 32 AF XY: 0.546 AC XY: 40552 AN XY: 74302

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.573

Alfa AF: 0.611 Hom.: 44845

Bravo AF: 0.539

Asia WGS AF: 0.623 AC: 2166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.3
Dann	Benign	0.48

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: rs940261; hg19: chr7-152545351;