7-36154948-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_030636.3(EEPD1):​c.624C>A​(p.Asn208Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

EEPD1
NM_030636.3 missense

Scores

1
5
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -2.51
Variant links:
Genes affected
EEPD1 (HGNC:22223): (endonuclease/exonuclease/phosphatase family domain containing 1) Predicted to enable DNA binding activity. Involved in positive regulation of cholesterol efflux. Is anchored component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

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
EEPD1NM_030636.3 linkc.624C>A p.Asn208Lys missense_variant Exon 2 of 8 ENST00000242108.9 NP_085139.2 Q7L9B9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EEPD1ENST00000242108.9 linkc.624C>A p.Asn208Lys missense_variant Exon 2 of 8 1 NM_030636.3 ENSP00000242108.4 Q7L9B9

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jan 27, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.624C>A (p.N208K) alteration is located in exon 2 (coding exon 1) of the EEPD1 gene. This alteration results from a C to A substitution at nucleotide position 624, causing the asparagine (N) at amino acid position 208 to be replaced by a lysine (K). 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
0.90
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.57
CADD
Benign
10
DANN
Uncertain
1.0
DEOGEN2
Benign
0.091
T;T
Eigen
Benign
-0.24
Eigen_PC
Benign
-0.35
FATHMM_MKL
Benign
0.32
N
LIST_S2
Uncertain
0.88
.;D
M_CAP
Benign
0.015
T
MetaRNN
Uncertain
0.65
D;D
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.1
L;L
PrimateAI
Uncertain
0.68
T
PROVEAN
Benign
-2.1
N;N
REVEL
Benign
0.18
Sift
Uncertain
0.011
D;D
Sift4G
Benign
0.062
T;T
Polyphen
0.99
D;D
Vest4
0.85
MutPred
0.39
Loss of sheet (P = 1e-04);Loss of sheet (P = 1e-04);
MVP
0.37
MPC
1.4
ClinPred
0.88
D
GERP RS
-1.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.22
gMVP
0.76

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-36194557; API