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19-18450663-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_006532.4(ELL):c.1279C>T(p.Leu427=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.01 in 1,591,648 control chromosomes in the GnomAD database, including 213 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.024 ( 95 hom., cov: 33)
Exomes 𝑓: 0.0085 ( 118 hom. )

Consequence

ELL
NM_006532.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.58
Variant links:
Genes affected
ELL (HGNC:23114): (elongation factor for RNA polymerase II) Enables phosphatase binding activity. Involved in positive regulation of transcription, DNA-templated and snRNA transcription. Located in cytosol; nuclear body; and transcriptionally active chromatin. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-18450663-G-A is Benign according to our data. Variant chr19-18450663-G-A is described in ClinVar as [Benign]. Clinvar id is 1304815.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.58 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0643 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ELLNM_006532.4 linkuse as main transcriptc.1279C>T p.Leu427= synonymous_variant 8/12 ENST00000262809.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ELLENST00000262809.9 linkuse as main transcriptc.1279C>T p.Leu427= synonymous_variant 8/121 NM_006532.4 P1
ELLENST00000596124.3 linkuse as main transcriptc.880C>T p.Leu294= synonymous_variant 8/121
ELLENST00000594635.6 linkuse as main transcriptc.*1114C>T 3_prime_UTR_variant, NMD_transcript_variant 9/131

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0239
AC:
3635
AN:
152170
Hom.:
92
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0661
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0146
Gnomad ASJ
AF:
0.00835
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00631
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00772
Gnomad OTH
AF:
0.0225
GnomAD3 exomes
AF:
0.00972
AC:
1963
AN:
202030
Hom.:
21
AF XY:
0.00834
AC XY:
921
AN XY:
110368
show subpopulations
Gnomad AFR exome
AF:
0.0685
Gnomad AMR exome
AF:
0.00723
Gnomad ASJ exome
AF:
0.00810
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000577
Gnomad FIN exome
AF:
0.00601
Gnomad NFE exome
AF:
0.00813
Gnomad OTH exome
AF:
0.00689
GnomAD4 exome
AF:
0.00855
AC:
12304
AN:
1439360
Hom.:
118
Cov.:
32
AF XY:
0.00817
AC XY:
5834
AN XY:
714464
show subpopulations
Gnomad4 AFR exome
AF:
0.0696
Gnomad4 AMR exome
AF:
0.00749
Gnomad4 ASJ exome
AF:
0.00736
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000510
Gnomad4 FIN exome
AF:
0.00691
Gnomad4 NFE exome
AF:
0.00762
Gnomad4 OTH exome
AF:
0.0109
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0240
AC:
3657
AN:
152288
Hom.:
95
Cov.:
33
AF XY:
0.0230
AC XY:
1710
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.0664
Gnomad4 AMR
AF:
0.0146
Gnomad4 ASJ
AF:
0.00835
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00631
Gnomad4 NFE
AF:
0.00772
Gnomad4 OTH
AF:
0.0222
Alfa
AF:
0.00816
Hom.:
2
Bravo
AF:
0.0264
Asia WGS
AF:
0.00837
AC:
29
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 22, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
3.4
Dann
Benign
0.66

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

LitVar

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

Other links and lift over

dbSNP: rs34868531; hg19: chr19-18561473; API