rs9552271

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr13-20747968-C-A
• chr13-20747968-C-G
• chr13-20747968-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001318939.2(EEF1AKMT1):​c.144+9487G>T 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

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

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

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.15
DANN	Benign	0.51

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;