19-38624117-GCC-ACG

Variant names:

• chr19-38624117-GCC-ACG
• NM_013234.4:c.199_201delGCCinsACG
• EIF3K p.Ala67Thr

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_013234.4(EIF3K):​c.199_201delGCCinsACG​(p.Ala67Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: EIF3K NM_013234.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.33
• Publications: 0 publications found

Genes affected

EIF3K (HGNC:24656): (eukaryotic translation initiation factor 3 subunit K) The 700-kD eukaryotic translation initiation factor-3 (eIF3) is the largest eIF and contains at least 12 subunits, including EIF2S12. eIF3 plays an essential role in translation by binding directly to the 40S ribosomal subunit and promoting formation of the 40S preinitiation complex (Mayeur et al., 2003 [PubMed 14519125]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013234.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EIF3K	NM_013234.4	MANE Select	c.199_201delGCCinsACG	p.Ala67Thr	missense	N/A	NP_037366.1	Q9UBQ5-1
	EIF3K	NM_001300992.2		c.199_201delGCCinsACG	p.Ala67Thr	missense	N/A	NP_001287921.1	K7ERF1
	EIF3K	NM_001308393.2		c.-63_-61delGCCinsACG		5_prime_UTR	Exon 3 of 8	NP_001295322.1	K7EK53

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EIF3K	ENST00000248342.9	TSL:1 MANE Select	c.199_201delGCCinsACG	p.Ala67Thr	missense	N/A	ENSP00000248342.3	Q9UBQ5-1
	EIF3K	ENST00000614624.4	TSL:1	c.100_102delGCCinsACG	p.Ala34Thr	missense	N/A	ENSP00000479334.1	A0A087WVB9
	EIF3K	ENST00000914932.1		c.199_201delGCCinsACG	p.Ala67Thr	missense	N/A	ENSP00000584991.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr19-39114757;