12-57781418-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.*772C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,496 control chromosomes in the GnomAD database, including 6,755 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 (6755 hom., cov: 30)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: EEF1AKMT3 NM_015433.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• 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	UniProt
EEF1AKMT3	NM_015433.3	c.*772C>T		3_prime_UTR_variant	3/3	ENST00000300209.13
EEF1AKMT3	NM_206914.2	c.*1142C>T		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EEF1AKMT3	ENST00000300209.13	c.*772C>T		3_prime_UTR_variant	3/3	1	NM_015433.3	P1
EEF1AKMT3	ENST00000333012.5	c.*1142C>T		3_prime_UTR_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40240 AN: 151366 Hom.: 6753 Cov.: 30

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.0833 AC: 1 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 NFE exome AF: 0.0833

GnomAD4 genome AF: 0.266 AC: 40247 AN: 151484 Hom.: 6755 Cov.: 30 AF XY: 0.274 AC XY: 20260 AN XY: 73974

Gnomad4 AFR AF: 0.0792

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.237

Alfa AF: 0.295 Hom.: 6940

Bravo AF: 0.247

Asia WGS AF: 0.519 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.5
Dann	Benign	0.59

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: rs11172335; hg19: chr12-58175201;