12-57781418-C-T

Variant names:

• chr12-57781418-C-T
• rs11172335
• NM_015433.3:c.*772C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015433.3(EEF1AKMT3):​c.*772C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,496 control chromosomes in the GnomAD database, including 6,755 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 0.27 (6755 hom., cov: 30)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: EEF1AKMT3 NM_015433.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550
• Publications: 31 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1AKMT3	NM_015433.3	c.*772C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000300209.13	NP_056248.2
EEF1AKMT3	NM_206914.2	c.*1142C>T		3_prime_UTR_variant	Exon 4 of 4		NP_996797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1AKMT3	ENST00000300209.13	c.*772C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_015433.3	ENSP00000300209.8
ENSG00000257921	ENST00000546504.1	c.77-1692C>T		intron_variant	Intron 1 of 3	2		ENSP00000449544.1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40240 AN: 151366 Hom.: 6753 Cov.: 30

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.0833 AC: 1 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0833 AC: 1 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.266 AC: 40247 AN: 151484 Hom.: 6755 Cov.: 30 AF XY: 0.274 AC XY: 20260 AN XY: 73974

African (AFR) AF: 0.0792 AC: 3270 AN: 41278

American (AMR) AF: 0.256 AC: 3907 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 989 AN: 3462

East Asian (EAS) AF: 0.651 AC: 3341 AN: 5130

South Asian (SAS) AF: 0.499 AC: 2392 AN: 4792

European-Finnish (FIN) AF: 0.377 AC: 3928 AN: 10412

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21533 AN: 67884

Other (OTH) AF: 0.237 AC: 495 AN: 2090

Alfa AF: 0.276 Hom.: 11161

Bravo AF: 0.247

Asia WGS AF: 0.519 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		-0.55
Mutation Taster		=99/1	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: rs11172335; hg19: chr12-58175201;