NM_015433.3:c.-105T>A

Variant names:

• chr12-57772620-T-A
• rs2291617
• NM_015433.3:c.-105T>A

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_015433.3(EEF1AKMT3):​c.-105T>A variant causes a 5 prime UTR 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: EEF1AKMT3 NM_015433.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635
• Publications: 45 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1AKMT3	NM_015433.3	c.-105T>A		5_prime_UTR_variant	Exon 1 of 3	ENST00000300209.13	NP_056248.2
EEF1AKMT3	NM_206914.2	c.-105T>A		5_prime_UTR_variant	Exon 1 of 4		NP_996797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1AKMT3	ENST00000300209.13	c.-105T>A		5_prime_UTR_variant	Exon 1 of 3	1	NM_015433.3	ENSP00000300209.8

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1124200 Hom.: 0 Cov.: 15 AF XY: 0.00 AC XY: 0 AN XY: 554202

African (AFR) AF: 0.00 AC: 0 AN: 25018

American (AMR) AF: 0.00 AC: 0 AN: 21818

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18230

East Asian (EAS) AF: 0.00 AC: 0 AN: 33880

South Asian (SAS) AF: 0.00 AC: 0 AN: 61770

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38042

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3356

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 874016

Other (OTH) AF: 0.00 AC: 0 AN: 48070

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 9865

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		0.64
PromoterAI		0.028	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.32		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.32		Position offset: 2

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

Other links and lift over

dbSNP: rs2291617; hg19: chr12-58166403;