rs10510102

chr10-121865675-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.975+4331A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,084 control chromosomes in the GnomAD database, including 2,264 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 0.17 (2264 hom., cov: 32)
• Consequence: ATE1 NM_001001976.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATE1	NM_001001976.3	c.975+4331A>G		intron_variant		ENST00000224652.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATE1	ENST00000224652.12	c.975+4331A>G		intron_variant		1	NM_001001976.3	A1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26194 AN: 151966 Hom.: 2262 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.172 AC: 26204 AN: 152084 Hom.: 2264 Cov.: 32 AF XY: 0.171 AC XY: 12678 AN XY: 74336

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.198

Alfa AF: 0.186 Hom.: 6243

Bravo AF: 0.173

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	7.9
Dann	Benign	0.70

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: rs10510102; hg19: chr10-123625190;