ENST00000333775.9:c.199T>A

Variant names:

• chr17-7857225-A-T
• rs923486015
• ENST00000333775.9:c.199T>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000333775.9(NAA38):​c.199T>A​(p.Ser67Thr) variant causes a missense 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. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: NAA38 ENST00000333775.9 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.49
• Publications: 0 publications found

Genes affected

NAA38 (HGNC:28212): (N-alpha-acetyltransferase 38, NatC auxiliary subunit) Involved in negative regulation of apoptotic process. Located in cytoplasm and nucleoplasm. Part of NatC complex. Colocalizes with polysome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.096304476).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000333775.9. 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
	NAA38	NM_001320925.4	MANE Select	c.82-27T>A		intron	N/A	NP_001307854.1	Q9BRA0-1
	NAA38	NM_032356.6		c.199T>A	p.Ser67Thr	missense	Exon 1 of 2	NP_115732.2
	NAA38	NM_001320924.3		c.82-27T>A		intron	N/A	NP_001307853.1	I3L3Z2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAA38	ENST00000333775.9	TSL:1	c.199T>A	p.Ser67Thr	missense	Exon 1 of 2	ENSP00000332103.5	Q9BRA0-2
	NAA38	ENST00000575771.6	TSL:1 MANE Select	c.82-27T>A		intron	N/A	ENSP00000460172.2	Q9BRA0-1
	NAA38	ENST00000576384.1	TSL:2	c.-102T>A		5_prime_UTR	Exon 1 of 2	ENSP00000460085.1	I3L310

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
PhyloP100		1.5
PromoterAI		0.0034	Neutral
gMVP		0.17

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

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

Other links and lift over

dbSNP: rs923486015; hg19: chr17-7760543;