8-28136724-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018091.6(ELP3):​c.907-974T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,100 control chromosomes in the GnomAD database, including 28,197 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 0.59 ( 28197 hom., cov: 32)

Consequence

ELP3
NM_018091.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.37
Variant links:
Genes affected
ELP3 (HGNC:20696): (elongator acetyltransferase complex subunit 3) Enables acetyltransferase activity and phosphorylase kinase regulator activity. Involved in regulation of transcription by RNA polymerase II and tRNA wobble uridine modification. Located in cytosol and nucleolus. Part of elongator holoenzyme complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ELP3NM_018091.6 linkuse as main transcriptc.907-974T>G intron_variant ENST00000256398.13 NP_060561.3 Q9H9T3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ELP3ENST00000256398.13 linkuse as main transcriptc.907-974T>G intron_variant 1 NM_018091.6 ENSP00000256398.8 Q9H9T3-1

Frequencies

GnomAD3 genomes
AF:
0.587
AC:
89204
AN:
151982
Hom.:
28138
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.786
Gnomad AMI
AF:
0.343
Gnomad AMR
AF:
0.651
Gnomad ASJ
AF:
0.404
Gnomad EAS
AF:
0.920
Gnomad SAS
AF:
0.577
Gnomad FIN
AF:
0.492
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.456
Gnomad OTH
AF:
0.554
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.587
AC:
89329
AN:
152100
Hom.:
28197
Cov.:
32
AF XY:
0.593
AC XY:
44104
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.786
Gnomad4 AMR
AF:
0.651
Gnomad4 ASJ
AF:
0.404
Gnomad4 EAS
AF:
0.920
Gnomad4 SAS
AF:
0.578
Gnomad4 FIN
AF:
0.492
Gnomad4 NFE
AF:
0.456
Gnomad4 OTH
AF:
0.559
Alfa
AF:
0.507
Hom.:
9652
Bravo
AF:
0.609
Asia WGS
AF:
0.744
AC:
2583
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.27
DANN
Benign
0.55

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: rs4732828; hg19: chr8-27994241; API