rs9860874

chr3-169768483-C-Achr3-169768483-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACTRT3	NM_032487.5	c.201-133G>T		intron_variant		ENST00000330368.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACTRT3	ENST00000330368.3	c.201-133G>T		intron_variant		1	NM_032487.5	P1

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

Gnomad4 AFR exome AF: 0.367

Gnomad4 AMR exome AF: 0.464

Gnomad4 ASJ exome AF: 0.233

Gnomad4 EAS exome AF: 0.717

Gnomad4 SAS exome AF: 0.387

Gnomad4 FIN exome AF: 0.288

Gnomad4 NFE exome AF: 0.247

Gnomad4 OTH exome AF: 0.301

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

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.338

Alfa AF: 0.280 Hom.: 2075

Bravo AF: 0.348

Asia WGS AF: 0.527 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.8
Dann	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs9860874; hg19: chr3-169486271;