rs893367

Variant names:

• chr3-53875704-C-A
• rs893367
• NM_022899.5:c.911+244G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-53875704-C-A
• chr3-53875704-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022899.5(ACTR8):​c.911+244G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,134 control chromosomes in the GnomAD database, including 25,998 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 0.57 (25998 hom., cov: 33)
• Consequence: ACTR8 NM_022899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 19 publications found

Genes affected

ACTR8 (HGNC:14672): (actin related protein 8) Predicted to enable ATP binding activity. Predicted to be involved in chromatin remodeling; double-strand break repair; and regulation of transcription, DNA-templated. Located in centrosome and nucleoplasm. Part of Ino80 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022899.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACTR8	NM_022899.5	MANE Select	c.911+244G>T		intron	N/A	NP_075050.3
	ACTR8	NM_001410774.1		c.578+244G>T		intron	N/A	NP_001397703.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACTR8	ENST00000335754.8	TSL:2 MANE Select	c.911+244G>T		intron	N/A	ENSP00000336842.3
	ACTR8	ENST00000482349.5	TSL:2	c.578+244G>T		intron	N/A	ENSP00000419429.1
	ACTR8	ENST00000486794.1	TSL:2	c.305+244G>T		intron	N/A	ENSP00000417230.1

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85880 AN: 152016 Hom.: 25939 Cov.: 33

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.565 AC: 85996 AN: 152134 Hom.: 25998 Cov.: 33 AF XY: 0.571 AC XY: 42438 AN XY: 74380

African (AFR) AF: 0.729 AC: 30257 AN: 41524

American (AMR) AF: 0.616 AC: 9410 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1513 AN: 3470

East Asian (EAS) AF: 0.949 AC: 4920 AN: 5184

South Asian (SAS) AF: 0.667 AC: 3214 AN: 4816

European-Finnish (FIN) AF: 0.429 AC: 4528 AN: 10564

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30354 AN: 67972

Other (OTH) AF: 0.536 AC: 1130 AN: 2110

Alfa AF: 0.487 Hom.: 80535

Bravo AF: 0.586

Asia WGS AF: 0.809 AC: 2813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.080
DANN	Benign	0.68
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs893367; hg19: chr3-53909731;