Genetic Variant EEF1AKMT3:c.-105T>G (chr12-57772620-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015433.3(EEF1AKMT3):c.-105T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 1,273,888 control chromosomes in the GnomAD database, including 79,311 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 0.29 ( 7491 hom., cov: 33)

Exomes 𝑓: 0.34 ( 71820 hom. )

Consequence

EEF1AKMT3
NM_015433.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.635

Publications

45 publications found

Variant links:

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]

EEF1AKMT3 links:

ENSG00000257921 (HGNC:):

ENSG00000257921 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015433.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1AKMT3	NM_015433.3	MANE Select	c.-105T>G		5_prime_UTR	Exon 1 of 3	NP_056248.2
	EEF1AKMT3	NM_206914.2		c.-105T>G		5_prime_UTR	Exon 1 of 4	NP_996797.1	Q96AZ1-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EEF1AKMT3	ENST00000300209.13	TSL:1 MANE Select	c.-105T>G	5_prime_UTR	Exon 1 of 3	ENSP00000300209.8	Q96AZ1-1
EEF1AKMT3	ENST00000548256.5	TSL:4	c.52-397T>G	intron	N/A	ENSP00000447718.1	F8VZI8
EEF1AKMT3	ENST00000551420.1	TSL:2	c.-367+223T>G	intron	N/A	ENSP00000448163.1	F8W226

Frequencies

GnomAD3 genomes

AF:

0.293

AC:

44579

AN:

151964

Hom.:

7472

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.286

Gnomad EAS

AF:

0.655

Gnomad SAS

AF:

0.566

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.262

GnomAD4 exome

AF:

0.345

AC:

386513

AN:

1121806

Hom.:

71820

Cov.:

AF XY:

0.350

AC XY:

193805

AN XY:

552996

show subpopulations

African (AFR)

AF:

0.152

AC:

3786

AN:

24982

American (AMR)

AF:

0.313

AC:

6819

AN:

21794

Ashkenazi Jewish (ASJ)

AF:

0.290

AC:

5283

AN:

18218

East Asian (EAS)

AF:

0.708

AC:

23964

AN:

33842

South Asian (SAS)

AF:

0.550

AC:

33923

AN:

61660

European-Finnish (FIN)

AF:

0.353

AC:

13398

AN:

37996

Middle Eastern (MID)

AF:

0.222

AC:

743

AN:

3348

European-Non Finnish (NFE)

AF:

0.324

AC:

282461

AN:

871968

Other (OTH)

AF:

0.336

AC:

16136

AN:

47998

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

11898

23796

35693

47591

59489

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9138

18276

27414

36552

45690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.293

AC:

44628

AN:

152082

Hom.:

7491

Cov.:

AF XY:

0.302

AC XY:

22451

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.164

AC:

6796

AN:

41514

American (AMR)

AF:

0.268

AC:

4099

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.286

AC:

992

AN:

3470

East Asian (EAS)

AF:

0.655

AC:

3370

AN:

5148

South Asian (SAS)

AF:

0.567

AC:

2736

AN:

4826

European-Finnish (FIN)

AF:

0.378

AC:

3998

AN:

10582

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.319

AC:

21678

AN:

67934

Other (OTH)

AF:

0.269

AC:

566

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1605

3210

4814

6419

8024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

472

944

1416

1888

2360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.301

Hom.:

9865

Bravo

AF:

0.276

Asia WGS

AF:

0.594

AC:

2061

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

0.64

PromoterAI

-0.12

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over