NM_016045.3:c.20A>G

Variant names:

• chr20-59042711-T-C
• NM_016045.3:c.20A>G

Variant summary

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

The NM_016045.3(PRELID3B):​c.20A>G​(p.Glu7Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: PRELID3B NM_016045.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.34
• Publications: 0 publications found

Genes affected

PRELID3B (HGNC:15892): (PRELI domain containing 3B) Predicted to enable phosphatidic acid transfer activity. Predicted to be involved in phospholipid transport. Predicted to be active in mitochondrial intermembrane space. [provided by Alliance of Genome Resources, Apr 2022]

SLMO2-ATP5E (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016045.3. 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
	PRELID3B	NM_016045.3	MANE Select	c.20A>G	p.Glu7Gly	missense	Exon 1 of 6	NP_057129.2	Q9Y3B1-1
	PRELID3B	NM_001256403.2		c.20A>G	p.Glu7Gly	missense	Exon 1 of 5	NP_001243332.1	Q9Y3B1-2
	SLMO2-ATP5E	NR_037929.1		n.136A>G		non_coding_transcript_exon	Exon 1 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRELID3B	ENST00000355937.9	TSL:1 MANE Select	c.20A>G	p.Glu7Gly	missense	Exon 1 of 6	ENSP00000348206.4	Q9Y3B1-1
	PRELID3B	ENST00000852164.1		c.20A>G	p.Glu7Gly	missense	Exon 1 of 6	ENSP00000522223.1
	PRELID3B	ENST00000371033.9	TSL:2	c.20A>G	p.Glu7Gly	missense	Exon 1 of 5	ENSP00000360072.5	Q9Y3B1-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

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	Pathogenic	0.72
BayesDel_addAF	Benign	0.0061	T
BayesDel_noAF	Benign	-0.23
CADD	Pathogenic	33
DANN	Uncertain	1.0
DEOGEN2	Benign	0.14	T
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.37
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.94	D
M_CAP	Uncertain	0.18	D
MetaRNN	Uncertain	0.59	D
MetaSVM	Benign	-1.0	T
PhyloP100		6.3
PrimateAI	Uncertain	0.78	T
PROVEAN	Pathogenic	-5.6	D
REVEL	Benign	0.23
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0090	D
Polyphen		0.57	P
Vest4		0.64
MutPred		0.41		Gain of MoRF binding (P = 0.0086)
MVP		0.52
MPC		0.44
ClinPred		1.0	D
GERP RS		5.1
PromoterAI		-0.18	Neutral
Varity_R		0.85
gMVP		0.59
Mutation Taster		=21/79	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

hg19: chr20-57617766;