9-127945742-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001035254.3(EEIG1):​c.628G>A​(p.Glu210Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 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)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

EEIG1
NM_001035254.3 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.01
Variant links:
Genes affected
EEIG1 (HGNC:31419): (estrogen-induced osteoclastogenesis regulator 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.15302989).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EEIG1NM_001035254.3 linkc.628G>A p.Glu210Lys missense_variant Exon 7 of 11 ENST00000373095.6 NP_001030331.1 Q5T9C2-1
EEIG1NM_203305.3 linkc.202G>A p.Glu68Lys missense_variant Exon 4 of 8 NP_976050.1 Q5T9C2-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EEIG1ENST00000373095.6 linkc.628G>A p.Glu210Lys missense_variant Exon 7 of 11 5 NM_001035254.3 ENSP00000362187.1 Q5T9C2-1
EEIG1ENST00000373084.8 linkc.202G>A p.Glu68Lys missense_variant Exon 4 of 8 1 ENSP00000362176.4 Q5T9C2-3
EEIG1ENST00000300434.3 linkn.312G>A non_coding_transcript_exon_variant Exon 2 of 6 1
EEIG1ENST00000465821.5 linkn.101G>A non_coding_transcript_exon_variant Exon 2 of 5 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1413436
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
698706
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
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
Dec 01, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.628G>A (p.E210K) alteration is located in exon 7 (coding exon 7) of the FAM102A gene. This alteration results from a G to A substitution at nucleotide position 628, causing the glutamic acid (E) at amino acid position 210 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
Benign
0.12
BayesDel_addAF
Benign
-0.00083
T
BayesDel_noAF
Benign
-0.24
CADD
Benign
22
DANN
Benign
0.95
DEOGEN2
Benign
0.057
T;.
Eigen
Benign
0.063
Eigen_PC
Benign
0.15
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.93
D;D
M_CAP
Benign
0.0058
T
MetaRNN
Benign
0.15
T;T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
2.0
M;.
PrimateAI
Uncertain
0.61
T
PROVEAN
Benign
-0.82
N;N
REVEL
Benign
0.14
Sift
Benign
0.80
T;T
Sift4G
Benign
0.90
T;T
Polyphen
0.80
P;.
Vest4
0.31
MutPred
0.16
Gain of ubiquitination at E210 (P = 0.0014);.;
MVP
0.33
MPC
0.45
ClinPred
0.83
D
GERP RS
4.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.20
gMVP
0.42

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: chr9-130708021; API