Variant chr18-36145968-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_018255.4(ELP2):c.913G>A(p.Val305Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 1,611,440 control chromosomes in the GnomAD database, including 103,372 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.36 ( 9965 hom., cov: 32)

Exomes 𝑓: 0.35 ( 93407 hom. )

Consequence

ELP2
NM_018255.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.286

Variant links:

Genes affected

ELP2 (HGNC:18248): (elongator acetyltransferase complex subunit 2) The protein encoded by this gene is a core subunit of the elongator complex, a histone acetyltransferase complex that associates with RNA polymerase II. In addition to histone acetylation, the encoded protein effects transcriptional elongation and may help remodel chromatin. [provided by RefSeq, May 2016]

ELP2 links:

ELP2 (HGNC:):

ELP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004386574).

BP6

Variant 18-36145968-G-A is Benign according to our data. Variant chr18-36145968-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELP2	NM_018255.4 linkuse as main transcript	c.913G>A	p.Val305Met	missense_variant	10/22	ENST00000358232.11	NP_060725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELP2	ENST00000358232.11 linkuse as main transcript	c.913G>A	p.Val305Met	missense_variant	10/22	1	NM_018255.4	ENSP00000350967.6		Q6IA86-1

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54740

AN:

151932

Hom.:

9967

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.392

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.367

GnomAD3 exomes

AF:

0.345

AC:

86750

AN:

251140

Hom.:

15567

AF XY:

0.338

AC XY:

45943

AN XY:

135740

show subpopulations

Gnomad AFR exome

AF:

0.377

Gnomad AMR exome

AF:

0.398

Gnomad ASJ exome

AF:

0.388

Gnomad EAS exome

AF:

0.186

Gnomad SAS exome

AF:

0.237

Gnomad FIN exome

AF:

0.363

Gnomad NFE exome

AF:

0.372

Gnomad OTH exome

AF:

0.370

GnomAD4 exome

AF:

0.354

AC:

517287

AN:

1459390

Hom.:

93407

Cov.:

AF XY:

0.351

AC XY:

254662

AN XY:

726136

show subpopulations

Gnomad4 AFR exome

AF:

0.378

Gnomad4 AMR exome

AF:

0.395

Gnomad4 ASJ exome

AF:

0.398

Gnomad4 EAS exome

AF:

0.200

Gnomad4 SAS exome

AF:

0.235

Gnomad4 FIN exome

AF:

0.360

Gnomad4 NFE exome

AF:

0.366

Gnomad4 OTH exome

AF:

0.347

GnomAD4 genome

AF:

0.360

AC:

54751

AN:

152050

Hom.:

9965

Cov.:

AF XY:

0.357

AC XY:

26550

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.370

Gnomad4 AMR

AF:

0.370

Gnomad4 ASJ

AF:

0.392

Gnomad4 EAS

AF:

0.197

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.360

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.365

Alfa

AF:

0.371

Hom.:

18329

Bravo

AF:

0.365

TwinsUK

AF:

0.354

AC:

1311

ALSPAC

AF:

0.367

AC:

1414

ESP6500AA

AF:

0.369

AC:

1626

ESP6500EA

AF:

0.371

AC:

3192

ExAC

AF:

0.343

AC:

41595

Asia WGS

AF:

0.258

AC:

900

AN:

3478

EpiCase

AF:

0.371

EpiControl

AF:

0.378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.062

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.53

CADD

Benign

4.6

DANN

Benign

0.18

DEOGEN2

Benign

0.017

T;.;.;.;.;.

Eigen

Benign

-0.98

Eigen_PC

Benign

-0.80

FATHMM_MKL

Benign

0.37

LIST_S2

Benign

0.68

T;T;T;T;T;T

MetaRNN

Benign

0.0044

T;T;T;T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

-1.4

N;.;.;.;.;.

PrimateAI

Benign

0.30

PROVEAN

Benign

1.4

N;N;N;N;N;N

REVEL

Benign

0.071

Sift

Benign

0.75

T;T;T;T;T;T

Sift4G

Benign

0.93

T;T;T;T;T;T

Polyphen

0.0

B;B;.;.;.;B

Vest4

0.14

MPC

0.080

ClinPred

0.0011

GERP RS

-1.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.023

gMVP

0.18

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over