rs2935706

Positions:

• chr10-121732153-G-C
• chr10-121732153-G-T

Variant summary

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

The ENST00000690984.1(ATE1):​c.437-22670C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,006 control chromosomes in the GnomAD database, including 6,837 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 0.29 (6837 hom., cov: 32)
• Consequence: ATE1 ENST00000690984.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

Genes affected

ATE1 (HGNC:782): (arginyltransferase 1) This gene encodes an arginyltransferase, an enzyme that is involved in posttranslational conjugation of arginine to N-terminal aspartate or glutamate residues. Conjugation of arginine to the N-terminal aspartate or glutamate targets proteins for ubiquitin-dependent degradation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATE1	ENST00000690984.1	c.437-22670C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43603 AN: 151888 Hom.: 6809 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.287 AC: 43667 AN: 152006 Hom.: 6837 Cov.: 32 AF XY: 0.294 AC XY: 21827 AN XY: 74280

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.280

Alfa AF: 0.260 Hom.: 715

Bravo AF: 0.293

Asia WGS AF: 0.291 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2935706; hg19: chr10-123491668;