13-20747968-C-T

Variant names:

• chr13-20747968-C-T
• rs9552271
• NM_001318939.2:c.144+9487G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001318939.2(EEF1AKMT1):​c.144+9487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 237,890 control chromosomes in the GnomAD database, including 20,544 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 0.38 (11982 hom., cov: 31)
  • Exomes 𝑓: 0.41 (8562 hom.)
• Consequence: EEF1AKMT1 NM_001318939.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

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]

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.736 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57452 AN: 151922 Hom.: 11954 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.316

GnomAD4 exome AF: 0.415 AC: 35602 AN: 85850 Hom.: 8562 Cov.: 0 AF XY: 0.405 AC XY: 21625 AN XY: 53394

Gnomad4 AFR exome AF: 0.371

Gnomad4 AMR exome AF: 0.685

Gnomad4 ASJ exome AF: 0.273

Gnomad4 EAS exome AF: 0.737

Gnomad4 SAS exome AF: 0.607

Gnomad4 FIN exome AF: 0.394

Gnomad4 NFE exome AF: 0.322

Gnomad4 OTH exome AF: 0.385

GnomAD4 genome AF: 0.378 AC: 57517 AN: 152040 Hom.: 11982 Cov.: 31 AF XY: 0.390 AC XY: 28959 AN XY: 74320

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.326

Alfa AF: 0.327 Hom.: 17789

Bravo AF: 0.381

Asia WGS AF: 0.667 AC: 2317 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	0.19
DANN	Benign	0.43

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

LitVar

Other links and lift over

dbSNP: rs9552271; hg19: chr13-21322107;