3-169768483-C-A

Variant names:

• chr3-169768483-C-A
• rs9860874
• NM_032487.5:c.201-133G>T

Variant summary

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

The NM_032487.5(ACTRT3):​c.201-133G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 839,502 control chromosomes in the GnomAD database, including 43,341 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 0.33 (8880 hom., cov: 31)
  • Exomes 𝑓: 0.29 (34461 hom.)
• Consequence: ACTRT3 NM_032487.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 19 publications found

Genes affected

ACTRT3 (HGNC:24022): (actin related protein T3) Predicted to be located in male germ cell nucleus. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032487.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACTRT3	NM_032487.5	MANE Select	c.201-133G>T		intron	N/A	NP_115876.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACTRT3	ENST00000330368.3	TSL:1 MANE Select	c.201-133G>T		intron	N/A	ENSP00000333037.1	Q9BYD9
	ACTRT3	ENST00000956146.1		c.201-133G>T		intron	N/A	ENSP00000626205.1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50027 AN: 151486 Hom.: 8856 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.334

GnomAD4 exome AF: 0.292 AC: 200577 AN: 687902 Hom.: 34461 AF XY: 0.296 AC XY: 103114 AN XY: 348656

African (AFR) AF: 0.367 AC: 6007 AN: 16356

American (AMR) AF: 0.464 AC: 8868 AN: 19122

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 3562 AN: 15258

East Asian (EAS) AF: 0.717 AC: 22857 AN: 31884

South Asian (SAS) AF: 0.387 AC: 18708 AN: 48374

European-Finnish (FIN) AF: 0.288 AC: 8640 AN: 30014

Middle Eastern (MID) AF: 0.324 AC: 815 AN: 2512

European-Non Finnish (NFE) AF: 0.247 AC: 120964 AN: 490660

Other (OTH) AF: 0.301 AC: 10156 AN: 33722

GnomAD4 genome AF: 0.330 AC: 50097 AN: 151600 Hom.: 8880 Cov.: 31 AF XY: 0.334 AC XY: 24747 AN XY: 74030

African (AFR) AF: 0.388 AC: 15984 AN: 41230

American (AMR) AF: 0.391 AC: 5968 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 769 AN: 3472

East Asian (EAS) AF: 0.684 AC: 3518 AN: 5146

South Asian (SAS) AF: 0.391 AC: 1882 AN: 4810

European-Finnish (FIN) AF: 0.273 AC: 2850 AN: 10426

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18106 AN: 67954

Other (OTH) AF: 0.338 AC: 710 AN: 2102

Alfa AF: 0.281 Hom.: 3350

Bravo AF: 0.348

Asia WGS AF: 0.527 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.65
PhyloP100		-0.12
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: rs9860874; hg19: chr3-169486271;