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GeneBe

11-31603860-A-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_019040.5(ELP4):c.606A>T(p.Gly202=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000606 in 1,611,780 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00059 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00061 ( 5 hom. )

Consequence

ELP4
NM_019040.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.122
Variant links:
Genes affected
ELP4 (HGNC:1171): (elongator acetyltransferase complex subunit 4) This gene encodes a component of the six subunit elongator complex, a histone acetyltransferase complex that associates directly with RNA polymerase II during transcriptional elongation. The human gene can partially complement sensitivity phenotypes of yeast ELP4 deletion mutants. This gene has also been associated with Rolandic epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 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=-0.53).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-31603860-A-T is Benign according to our data. Variant chr11-31603860-A-T is described in ClinVar as [Benign]. Clinvar id is 2801587.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=0.122 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 89 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ELP4NM_019040.5 linkuse as main transcriptc.606A>T p.Gly202= synonymous_variant 5/10 ENST00000640961.2
ELP4NM_001288726.2 linkuse as main transcriptc.606A>T p.Gly202= synonymous_variant 5/12
ELP4NM_001288725.2 linkuse as main transcriptc.609A>T p.Gly203= synonymous_variant 5/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ELP4ENST00000640961.2 linkuse as main transcriptc.606A>T p.Gly202= synonymous_variant 5/101 NM_019040.5 P3Q96EB1-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000586
AC:
89
AN:
151800
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.000866
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00264
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000812
Gnomad OTH
AF:
0.000961
GnomAD3 exomes
AF:
0.00105
AC:
261
AN:
248690
Hom.:
2
AF XY:
0.00101
AC XY:
136
AN XY:
134974
show subpopulations
Gnomad AFR exome
AF:
0.000129
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.000995
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00172
Gnomad NFE exome
AF:
0.00184
Gnomad OTH exome
AF:
0.000828
GnomAD4 exome
AF:
0.000608
AC:
888
AN:
1459980
Hom.:
5
Cov.:
30
AF XY:
0.000587
AC XY:
426
AN XY:
726302
show subpopulations
Gnomad4 AFR exome
AF:
0.000120
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.000998
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00247
Gnomad4 NFE exome
AF:
0.000614
Gnomad4 OTH exome
AF:
0.000730
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000586
AC:
89
AN:
151800
Hom.:
1
Cov.:
32
AF XY:
0.000540
AC XY:
40
AN XY:
74114
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.000866
Gnomad4 EAS
AF:
0.000192
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00264
Gnomad4 NFE
AF:
0.000812
Gnomad4 OTH
AF:
0.000961
Alfa
AF:
0.00130
Hom.:
1
Bravo
AF:
0.000276
EpiCase
AF:
0.000164
EpiControl
AF:
0.000534

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 testingInvitaeOct 28, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
Cadd
Benign
11
Dann
Benign
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
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: rs376912655; hg19: chr11-31625407; API