rs11200251

chr10-121913691-C-T

Variant summary

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

The NM_001001976.3(ATE1):c.337+99G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 753,452 control chromosomes in the GnomAD database, including 42,405 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 0.30 (7119 hom., cov: 32)
  • Exomes 𝑓: 0.34 (35286 hom.)
• Consequence: ATE1 NM_001001976.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATE1	NM_001001976.3	c.337+99G>A		intron_variant		ENST00000224652.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATE1	ENST00000224652.12	c.337+99G>A		intron_variant		1	NM_001001976.3	A1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44882 AN: 151880 Hom.: 7105 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.303

GnomAD4 exome AF: 0.339 AC: 203880 AN: 601454 Hom.: 35286 AF XY: 0.343 AC XY: 107670 AN XY: 313688

Gnomad4 AFR exome AF: 0.164

Gnomad4 AMR exome AF: 0.362

Gnomad4 ASJ exome AF: 0.284

Gnomad4 EAS exome AF: 0.314

Gnomad4 SAS exome AF: 0.418

Gnomad4 FIN exome AF: 0.300

Gnomad4 NFE exome AF: 0.345

Gnomad4 OTH exome AF: 0.318

GnomAD4 genome AF: 0.296 AC: 44923 AN: 151998 Hom.: 7119 Cov.: 32 AF XY: 0.298 AC XY: 22157 AN XY: 74258

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.301

Alfa AF: 0.321 Hom.: 2070

Bravo AF: 0.288

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.5
Dann	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs11200251; hg19: chr10-123673206;