Genetic Variant EEF1AKMT1:c.144+9487G>T (chr13-20747968-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001318939.2(EEF1AKMT1):c.144+9487G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

EEF1AKMT1
NM_001318939.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.216

Publications

7 publications found

Variant links:

Genes affected

EEF1AKMT1 (HGNC:27351): (EEF1A lysine methyltransferase 1) Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine methylation. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

EEF1AKMT1 links:

RANP8 (HGNC:39863): (RAN pseudogene 8)

RANP8 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1AKMT1	NM_001318939.2 link	c.144+9487G>T		intron_variant	Intron 2 of 4	ENST00000382758.6	NP_001305868.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
EEF1AKMT1	ENST00000382758.6 link	c.144+9487G>T	intron_variant	Intron 2 of 4	1	NM_001318939.2	ENSP00000372206.1
EEF1AKMT1	ENST00000382754.4 link	c.144+9487G>T	intron_variant	Intron 2 of 4	1		ENSP00000372202.4
RANP8	ENST00000444720.1 link	n.90G>T	non_coding_transcript_exon_variant	Exon 1 of 2	6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

86378

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

53728

African (AFR)

AF:

0.00

AC:

AN:

1838

American (AMR)

AF:

0.00

AC:

AN:

7960

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1196

East Asian (EAS)

AF:

0.00

AC:

AN:

4236

South Asian (SAS)

AF:

0.00

AC:

AN:

9082

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6954

Middle Eastern (MID)

AF:

0.00

AC:

AN:

204

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

51282

Other (OTH)

AF:

0.00

AC:

AN:

3626

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.15

(source)

DANN

Benign

0.51

PhyloP100

-0.22

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over