20-59042711-T-C

Variant names:

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

Variant summary

Our verdict is Uncertain significance. Variant got 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

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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRELID3B	NM_016045.3	c.20A>G	p.Glu7Gly	missense_variant	Exon 1 of 6	ENST00000355937.9	NP_057129.2
PRELID3B	NM_001256403.2	c.20A>G	p.Glu7Gly	missense_variant	Exon 1 of 5		NP_001243332.1
SLMO2-ATP5E	NR_037929.1	n.136A>G		non_coding_transcript_exon_variant	Exon 1 of 8
SLMO2-ATP5E	NR_037930.1	n.136A>G		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRELID3B	ENST00000355937.9	c.20A>G	p.Glu7Gly	missense_variant	Exon 1 of 6	1	NM_016045.3	ENSP00000348206.4
PRELID3B	ENST00000371033.9	c.20A>G	p.Glu7Gly	missense_variant	Exon 1 of 5	2		ENSP00000360072.5
PRELID3B	ENST00000463057.1	n.20A>G		non_coding_transcript_exon_variant	Exon 1 of 6	3		ENSP00000431440.1
PRELID3B	ENST00000466051.1	n.99A>G		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Mar 06, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.20A>G (p.E7G) alteration is located in exon 1 (coding exon 1) of the PRELID3B gene. This alteration results from a A to G substitution at nucleotide position 20, causing the glutamic acid (E) at amino acid position 7 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

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;D
M_CAP	Uncertain	0.18	D
MetaRNN	Uncertain	0.59	D;D
MetaSVM	Benign	-1.0	T
PrimateAI	Uncertain	0.78	T
PROVEAN	Pathogenic	-5.6	D;D
REVEL	Benign	0.23
Sift	Uncertain	0.0010	D;D
Sift4G	Uncertain	0.0090	D;D
Polyphen		0.57	P;.
Vest4		0.64
MutPred		0.41		Gain of MoRF binding (P = 0.0086);Gain of MoRF binding (P = 0.0086);
MVP		0.52
MPC		0.44
ClinPred		1.0	D
GERP RS		5.1
Varity_R		0.85
gMVP		0.59

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-57617766;