rs8181644

Positions:

• chr12-57779683-T-C
• chr12-57779683-T-G

Variant summary

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

The NM_015433.3(EEF1AKMT3):​c.290-572T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,168 control chromosomes in the GnomAD database, including 7,154 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 0.28 (7154 hom., cov: 32)
• Consequence: EEF1AKMT3 NM_015433.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EEF1AKMT3	NM_015433.3	c.290-572T>C		intron_variant		ENST00000300209.13	NP_056248.2
EEF1AKMT3	NM_206914.2	c.429-572T>C		intron_variant			NP_996797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EEF1AKMT3	ENST00000300209.13	c.290-572T>C		intron_variant		1	NM_015433.3	ENSP00000300209.8
ENSG00000257921	ENST00000546504.1	c.77-3427T>C		intron_variant		2		ENSP00000449544.1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42145 AN: 152050 Hom.: 7136 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.277 AC: 42199 AN: 152168 Hom.: 7154 Cov.: 32 AF XY: 0.286 AC XY: 21295 AN XY: 74386

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.256

Alfa AF: 0.282 Hom.: 1346

Bravo AF: 0.257

Asia WGS AF: 0.594 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	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

Publications

LitVar

Other links and lift over

dbSNP: rs8181644; hg19: chr12-58173466;