13-20747968-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

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 = 0.736 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

African (AFR) AF: 0.371 AC: 676 AN: 1824

American (AMR) AF: 0.685 AC: 5429 AN: 7920

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 326 AN: 1192

East Asian (EAS) AF: 0.737 AC: 3100 AN: 4204

South Asian (SAS) AF: 0.607 AC: 5480 AN: 9030

European-Finnish (FIN) AF: 0.394 AC: 2721 AN: 6914

Middle Eastern (MID) AF: 0.299 AC: 61 AN: 204

European-Non Finnish (NFE) AF: 0.322 AC: 16424 AN: 50964

Other (OTH) AF: 0.385 AC: 1385 AN: 3598

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

African (AFR) AF: 0.373 AC: 15456 AN: 41458

American (AMR) AF: 0.481 AC: 7349 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 921 AN: 3472

East Asian (EAS) AF: 0.756 AC: 3899 AN: 5160

South Asian (SAS) AF: 0.628 AC: 3026 AN: 4820

European-Finnish (FIN) AF: 0.397 AC: 4198 AN: 10568

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21809 AN: 67972

Other (OTH) AF: 0.326 AC: 689 AN: 2116

Alfa AF: 0.333 Hom.: 25957

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
PhyloP100		-0.22
Mutation Taster		=100/0	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: rs9552271; hg19: chr13-21322107;