rs1874664

Positions:

• chr10-121742217-T-C

Variant summary

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

The NM_001001976.3(ATE1):​c.*1463A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,238 control chromosomes in the GnomAD database, including 2,362 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 0.16 (2362 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ATE1 NM_001001976.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATE1	NM_001001976.3	c.*1463A>G		3_prime_UTR_variant	12/12	ENST00000224652.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATE1	ENST00000224652.12	c.*1463A>G		3_prime_UTR_variant	12/12	1	NM_001001976.3	A1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24958 AN: 152120 Hom.: 2354 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.150

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.164 AC: 24994 AN: 152238 Hom.: 2362 Cov.: 33 AF XY: 0.170 AC XY: 12664 AN XY: 74430

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0708

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.159

Alfa AF: 0.126 Hom.: 2767

Bravo AF: 0.171

Asia WGS AF: 0.185 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.32

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: rs1874664; hg19: chr10-123501732;