rs56216502

Variant names:

• chr7-152802737-G-A
• rs4726211
• NM_020445.6:c.336+1006G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ACTR3B	NM_020445.6	c.336+1006G>A		intron_variant	Intron 4 of 11	ENST00000256001.13	NP_065178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACTR3B	ENST00000256001.13	c.336+1006G>A		intron_variant	Intron 4 of 11	1	NM_020445.6	ENSP00000256001.8
ACTR3B	ENST00000377776.7	c.336+1006G>A		intron_variant	Intron 4 of 9	1		ENSP00000367007.3
ACTR3B	ENST00000397282.2	c.72+1006G>A		intron_variant	Intron 3 of 10	2		ENSP00000380452.2
ACTR3B	ENST00000488782.1	n.144+1006G>A		intron_variant	Intron 2 of 4	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

African (AFR) AF: 0.157 AC: 6511 AN: 41396

American (AMR) AF: 0.605 AC: 9231 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2002 AN: 3470

East Asian (EAS) AF: 0.715 AC: 3684 AN: 5152

South Asian (SAS) AF: 0.525 AC: 2526 AN: 4812

European-Finnish (FIN) AF: 0.580 AC: 6107 AN: 10534

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35527 AN: 67932

Other (OTH) AF: 0.488 AC: 1027 AN: 2106

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
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4726211; hg19: chr7-152499822;