rs56216502

Positions:

• chr7-152802737-G-A
• chr7-152802737-G-C

Variant summary

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

The NM_020445.6(ACTR3B):​c.336+1006G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,858 control chromosomes in the GnomAD database, including 17,552 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 0.44 (17552 hom., cov: 30)
• Consequence: ACTR3B NM_020445.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACTR3B	NM_020445.6	c.336+1006G>A		intron_variant		ENST00000256001.13	NP_065178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACTR3B	ENST00000256001.13	c.336+1006G>A		intron_variant		1	NM_020445.6	ENSP00000256001	P1
ACTR3B	ENST00000377776.7	c.336+1006G>A		intron_variant		1		ENSP00000367007
ACTR3B	ENST00000397282.2	c.72+1006G>A		intron_variant		2		ENSP00000380452
ACTR3B	ENST00000488782.1	n.144+1006G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67323 AN: 151740 Hom.: 17545 Cov.: 30

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.443 AC: 67339 AN: 151858 Hom.: 17552 Cov.: 30 AF XY: 0.452 AC XY: 33556 AN XY: 74204

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.488

Alfa AF: 0.470 Hom.: 2250

Bravo AF: 0.438

Asia WGS AF: 0.588 AC: 2040 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.55

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: rs4726211; hg19: chr7-152499822;