chr10-124749450-C-T

Position:

• chr10-124749450-C-T

Variant summary

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

The ENST00000495711.2(EEF1AKMT2):​c.*92-964G>A variant causes a intron, NMD transcript 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: EEF1AKMT2 ENST00000495711.2 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560

Genes affected

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EEF1AKMT2	ENST00000495711.2	c.*92-964G>A		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.0345

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.0691

Gnomad4 SAS AF: 0.0999

Gnomad4 FIN AF: 0.0254

Gnomad4 NFE AF: 0.0510

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0487 Hom.: 194

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

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: rs10510138; hg19: chr10-126438019;