12-57779146-C-T

Position:

• chr12-57779146-C-T

Variant summary

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

The NM_015433.3(EEF1AKMT3):​c.290-1109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,072 control chromosomes in the GnomAD database, including 6,792 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 0.27 (6792 hom., cov: 31)
• Consequence: EEF1AKMT3 NM_015433.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

Genes affected

EEF1AKMT3 (HGNC:24936): (EEF1A lysine methyltransferase 3) Enables heat shock protein binding activity and protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine methylation. Located in several cellular components, including centrosome; chromosome; and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000257921 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EEF1AKMT3	NM_015433.3	c.290-1109C>T		intron_variant		ENST00000300209.13	NP_056248.2
EEF1AKMT3	NM_206914.2	c.429-1109C>T		intron_variant			NP_996797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EEF1AKMT3	ENST00000300209.13	c.290-1109C>T		intron_variant		1	NM_015433.3	ENSP00000300209.8
ENSG00000257921	ENST00000546504.1	c.77-3964C>T		intron_variant		2		ENSP00000449544.1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40510 AN: 151954 Hom.: 6789 Cov.: 31

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.267 AC: 40529 AN: 152072 Hom.: 6792 Cov.: 31 AF XY: 0.275 AC XY: 20433 AN XY: 74306

Gnomad4 AFR AF: 0.0825

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.238

Alfa AF: 0.212 Hom.: 858

Bravo AF: 0.248

Asia WGS AF: 0.523 AC: 1816 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	0.67

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: rs10877019; hg19: chr12-58172929;