NM_001318939.2:c.144+9487G>C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001318939.2(EEF1AKMT1):​c.144+9487G>C 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
• 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: 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=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318939.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1AKMT1	NM_001318939.2	MANE Select	c.144+9487G>C		intron	N/A	NP_001305868.1
	EEF1AKMT1	NM_174928.3		c.144+9487G>C		intron	N/A	NP_777588.1
	EEF1AKMT1	NR_134934.2		n.204+9487G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEF1AKMT1	ENST00000382758.6	TSL:1 MANE Select	c.144+9487G>C		intron	N/A	ENSP00000372206.1
	EEF1AKMT1	ENST00000382754.4	TSL:1	c.144+9487G>C		intron	N/A	ENSP00000372202.4
	RANP8	ENST00000444720.1	TSL:6	n.90G>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 86378 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 53728

African (AFR) AF: 0.00 AC: 0 AN: 1838

American (AMR) AF: 0.00 AC: 0 AN: 7960

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1196

East Asian (EAS) AF: 0.00 AC: 0 AN: 4236

South Asian (SAS) AF: 0.00 AC: 0 AN: 9082

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6954

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 204

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 51282

Other (OTH) AF: 0.00 AC: 0 AN: 3626

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 25957

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.15
DANN	Benign	0.46
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

Other links and lift over

dbSNP: rs9552271; hg19: chr13-21322107;