rs8181644

Variant names:

• chr12-57779683-T-C
• rs8181644
• NM_015433.3:c.290-572T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
EEF1AKMT3	NM_015433.3	c.290-572T>C		intron_variant	Intron 2 of 2	ENST00000300209.13	NP_056248.2
EEF1AKMT3	NM_206914.2	c.429-572T>C		intron_variant	Intron 3 of 3		NP_996797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1AKMT3	ENST00000300209.13	c.290-572T>C		intron_variant	Intron 2 of 2	1	NM_015433.3	ENSP00000300209.8
ENSG00000257921	ENST00000546504.1	c.77-3427T>C		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.108 AC: 4482 AN: 41554

American (AMR) AF: 0.261 AC: 3997 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3462

East Asian (EAS) AF: 0.657 AC: 3393 AN: 5168

South Asian (SAS) AF: 0.567 AC: 2730 AN: 4818

European-Finnish (FIN) AF: 0.378 AC: 4000 AN: 10582

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21678 AN: 67982

Other (OTH) AF: 0.256 AC: 540 AN: 2112

Alfa AF: 0.278 Hom.: 1351

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
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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: rs8181644; hg19: chr12-58173466;