X-130069380-C-T

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001421.4(ELF4):​c.1107G>A​(p.Ser369Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00711 in 1,210,819 control chromosomes in the GnomAD database, including 35 homozygotes. There are 2,827 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0055 ( 3 hom., 181 hem., cov: 24)
Exomes 𝑓: 0.0073 ( 32 hom. 2646 hem. )

Consequence

ELF4
NM_001421.4 synonymous

Scores

9

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0870
Variant links:
Genes affected
ELF4 (HGNC:3319): (E74 like ETS transcription factor 4) The protein encoded by this gene is a transcriptional activator that binds and activates the promoters of the CSF2, IL3, IL8, and PRF1 genes. The encoded protein is involved in natural killer cell development and function, innate immunity, and induction of cell cycle arrest in naive CD8+ cells. Two transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Jan 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.004645109).
BP6
Variant X-130069380-C-T is Benign according to our data. Variant chrX-130069380-C-T is described in ClinVar as [Benign]. Clinvar id is 788344.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-130069380-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-0.087 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ELF4NM_001421.4 linkc.1107G>A p.Ser369Ser synonymous_variant 8/9 ENST00000308167.10 NP_001412.1 Q99607

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ELF4ENST00000308167.10 linkc.1107G>A p.Ser369Ser synonymous_variant 8/91 NM_001421.4 ENSP00000311280.6 Q99607
ELF4ENST00000335997.11 linkc.1107G>A p.Ser369Ser synonymous_variant 8/91 ENSP00000338608.7 Q99607

Frequencies

GnomAD3 genomes
AF:
0.00553
AC:
622
AN:
112540
Hom.:
3
Cov.:
24
AF XY:
0.00522
AC XY:
181
AN XY:
34702
show subpopulations
Gnomad AFR
AF:
0.00126
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00178
Gnomad ASJ
AF:
0.00678
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000727
Gnomad FIN
AF:
0.0139
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00848
Gnomad OTH
AF:
0.00465
GnomAD3 exomes
AF:
0.00588
AC:
1079
AN:
183429
Hom.:
3
AF XY:
0.00591
AC XY:
401
AN XY:
67863
show subpopulations
Gnomad AFR exome
AF:
0.00129
Gnomad AMR exome
AF:
0.00128
Gnomad ASJ exome
AF:
0.00588
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000419
Gnomad FIN exome
AF:
0.0133
Gnomad NFE exome
AF:
0.00898
Gnomad OTH exome
AF:
0.00596
GnomAD4 exome
AF:
0.00728
AC:
7991
AN:
1098229
Hom.:
32
Cov.:
34
AF XY:
0.00728
AC XY:
2646
AN XY:
363583
show subpopulations
Gnomad4 AFR exome
AF:
0.000833
Gnomad4 AMR exome
AF:
0.00156
Gnomad4 ASJ exome
AF:
0.00583
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000517
Gnomad4 FIN exome
AF:
0.0142
Gnomad4 NFE exome
AF:
0.00821
Gnomad4 OTH exome
AF:
0.00555
GnomAD4 genome
AF:
0.00552
AC:
621
AN:
112590
Hom.:
3
Cov.:
24
AF XY:
0.00521
AC XY:
181
AN XY:
34762
show subpopulations
Gnomad4 AFR
AF:
0.00125
Gnomad4 AMR
AF:
0.00177
Gnomad4 ASJ
AF:
0.00678
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000364
Gnomad4 FIN
AF:
0.0139
Gnomad4 NFE
AF:
0.00848
Gnomad4 OTH
AF:
0.00459
Alfa
AF:
0.00665
Hom.:
64
Bravo
AF:
0.00470
TwinsUK
AF:
0.00809
AC:
30
ALSPAC
AF:
0.00762
AC:
22
ESP6500AA
AF:
0.000522
AC:
2
ESP6500EA
AF:
0.00936
AC:
63
ExAC
AF:
0.00605
AC:
735
EpiCase
AF:
0.00971
EpiControl
AF:
0.00830

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 31, 2019- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.59
T
BayesDel_noAF
Benign
-0.61
CADD
Benign
3.7
DANN
Benign
0.64
DEOGEN2
Benign
0.017
T
FATHMM_MKL
Benign
0.053
N
LIST_S2
Benign
0.43
T
MetaRNN
Benign
0.0046
T
Sift4G
Benign
0.69
T
Vest4
0.068
MVP
0.51
GERP RS
2.4

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9282674; hg19: chrX-129203355; API