chr9-108889742-C-A
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003640.5(ELP1):c.3161-349G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 356,194 control chromosomes in the GnomAD database, including 7,881 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.22 ( 4012 hom., cov: 32)
Exomes 𝑓: 0.19 ( 3869 hom. )
Consequence
ELP1
NM_003640.5 intron
NM_003640.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0440
Genes affected
ELP1 (HGNC:5959): (elongator acetyltransferase complex subunit 1) The protein encoded by this gene is a scaffold protein and a regulator for three different kinases involved in proinflammatory signaling. The encoded protein can bind NF-kappa-B-inducing kinase and I-kappa-B kinases through separate domains and assemble them into an active kinase complex. Mutations in this gene have been associated with familial dysautonomia. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP1 | NM_003640.5 | c.3161-349G>T | intron_variant | ENST00000374647.10 | NP_003631.2 | |||
ELP1 | NM_001318360.2 | c.2819-349G>T | intron_variant | NP_001305289.1 | ||||
ELP1 | NM_001330749.2 | c.2114-349G>T | intron_variant | NP_001317678.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ELP1 | ENST00000374647.10 | c.3161-349G>T | intron_variant | 1 | NM_003640.5 | ENSP00000363779 | P1 |
Frequencies
GnomAD3 genomes AF: 0.218 AC: 33040AN: 151906Hom.: 4009 Cov.: 32
GnomAD3 genomes
AF:
AC:
33040
AN:
151906
Hom.:
Cov.:
32
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: 0.189 AC: 38678AN: 204170Hom.: 3869 AF XY: 0.193 AC XY: 21198AN XY: 110102
GnomAD4 exome
AF:
AC:
38678
AN:
204170
Hom.:
AF XY:
AC XY:
21198
AN XY:
110102
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.217 AC: 33063AN: 152024Hom.: 4012 Cov.: 32 AF XY: 0.218 AC XY: 16210AN XY: 74314
GnomAD4 genome
AF:
AC:
33063
AN:
152024
Hom.:
Cov.:
32
AF XY:
AC XY:
16210
AN XY:
74314
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
953
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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