chr6-31958823-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002904.6(NELFE):c.-9+69G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0306 in 659,354 control chromosomes in the GnomAD database, including 655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.031 ( 161 hom., cov: 33)
Exomes 𝑓: 0.030 ( 494 hom. )
Consequence
NELFE
NM_002904.6 intron
NM_002904.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.258
Publications
8 publications found
Genes affected
NELFE (HGNC:13974): (negative elongation factor complex member E) The protein encoded by this gene is part of a complex termed negative elongation factor (NELF) which represses RNA polymerase II transcript elongation. This protein bears similarity to nuclear RNA-binding proteins; however, it has not been demonstrated that this protein binds RNA. The protein contains a tract of alternating basic and acidic residues, largely arginine (R) and aspartic acid (D). The gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 6-31958823-C-T is Benign according to our data. Variant chr6-31958823-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 356299.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0308 (4686/152308) while in subpopulation NFE AF = 0.0361 (2454/68034). AF 95% confidence interval is 0.0349. There are 161 homozygotes in GnomAd4. There are 2575 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 161 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NELFE | NM_002904.6 | c.-9+69G>A | intron_variant | Intron 1 of 10 | ENST00000375429.8 | NP_002895.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0308 AC: 4686AN: 152190Hom.: 161 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
4686
AN:
152190
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0305 AC: 15464AN: 507046Hom.: 494 Cov.: 0 AF XY: 0.0290 AC XY: 7917AN XY: 273324 show subpopulations
GnomAD4 exome
AF:
AC:
15464
AN:
507046
Hom.:
Cov.:
0
AF XY:
AC XY:
7917
AN XY:
273324
show subpopulations
African (AFR)
AF:
AC:
77
AN:
14122
American (AMR)
AF:
AC:
264
AN:
27652
Ashkenazi Jewish (ASJ)
AF:
AC:
51
AN:
16750
East Asian (EAS)
AF:
AC:
6
AN:
31746
South Asian (SAS)
AF:
AC:
537
AN:
56244
European-Finnish (FIN)
AF:
AC:
4121
AN:
31726
Middle Eastern (MID)
AF:
AC:
30
AN:
3708
European-Non Finnish (NFE)
AF:
AC:
9717
AN:
296530
Other (OTH)
AF:
AC:
661
AN:
28568
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.513
Heterozygous variant carriers
0
828
1656
2483
3311
4139
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0308 AC: 4686AN: 152308Hom.: 161 Cov.: 33 AF XY: 0.0346 AC XY: 2575AN XY: 74464 show subpopulations
GnomAD4 genome
AF:
AC:
4686
AN:
152308
Hom.:
Cov.:
33
AF XY:
AC XY:
2575
AN XY:
74464
show subpopulations
African (AFR)
AF:
AC:
260
AN:
41566
American (AMR)
AF:
AC:
190
AN:
15308
Ashkenazi Jewish (ASJ)
AF:
AC:
6
AN:
3472
East Asian (EAS)
AF:
AC:
5
AN:
5186
South Asian (SAS)
AF:
AC:
60
AN:
4832
European-Finnish (FIN)
AF:
AC:
1592
AN:
10592
Middle Eastern (MID)
AF:
AC:
4
AN:
294
European-Non Finnish (NFE)
AF:
AC:
2454
AN:
68034
Other (OTH)
AF:
AC:
37
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
226
452
677
903
1129
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
13
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Trichohepatoenteric syndrome Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
not provided Benign:1
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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