10-124749450-C-T

Variant names:

• chr10-124749450-C-T
• rs10510138
• ENST00000494792.1:n.*23+10936G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000494792.1(ENSG00000258539):​n.*23+10936G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 152,274 control chromosomes in the GnomAD database, including 152 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 0.038 (152 hom., cov: 33)
• Consequence: ENSG00000258539 ENST00000494792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560
• Publications: 8 publications found

Genes affected

ENSG00000258539 (HGNC:):

EEF1AKMT2 (HGNC:33787): (EEF1A lysine methyltransferase 2) Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine methylation. Located in cytosol and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258539	ENST00000494792.1	n.*23+10936G>A		intron_variant	Intron 6 of 9	5		ENSP00000455755.1
EEF1AKMT2	ENST00000495711.2	n.*92-964G>A		intron_variant	Intron 1 of 1	2		ENSP00000470332.1

Frequencies

GnomAD3 genomes AF: 0.0379 AC: 5770 AN: 152156 Hom.: 152 Cov.: 33

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0698

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0510

Gnomad OTH AF: 0.0396

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

GnomAD4 genome AF: 0.0378 AC: 5763 AN: 152274 Hom.: 152 Cov.: 33 AF XY: 0.0376 AC XY: 2801 AN XY: 74448

African (AFR) AF: 0.0109 AC: 452 AN: 41556

American (AMR) AF: 0.0345 AC: 527 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.0691 AC: 359 AN: 5192

South Asian (SAS) AF: 0.0999 AC: 482 AN: 4824

European-Finnish (FIN) AF: 0.0254 AC: 269 AN: 10602

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0510 AC: 3472 AN: 68012

Other (OTH) AF: 0.0388 AC: 82 AN: 2116

Alfa AF: 0.0438 Hom.: 277

Bravo AF: 0.0361

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.68
PhyloP100		0.56

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

Other links and lift over

dbSNP: rs10510138; hg19: chr10-126438019;