Variant chr5-95900711-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_012081.6(ELL2):c.936C>T(p.Asp312=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,578,646 control chromosomes in the GnomAD database, including 58,797 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 0.29 ( 6543 hom., cov: 32)

Exomes 𝑓: 0.26 ( 52254 hom. )

Consequence

ELL2
NM_012081.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.271

Variant links:

Genes affected

ELL2 (HGNC:17064): (elongation factor for RNA polymerase II 2) Involved in snRNA transcription by RNA polymerase II. Located in nucleoplasm. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Apr 2022]

ELL2 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 (BayesDel_noAF=-0.92).

BP7

Synonymous conserved (PhyloP=-0.271 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELL2	NM_012081.6 linkuse as main transcript	c.936C>T	p.Asp312=	synonymous_variant	7/12	ENST00000237853.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELL2	ENST00000237853.9 linkuse as main transcript	c.936C>T	p.Asp312=	synonymous_variant	7/12	1	NM_012081.6	P1	O00472-1
ELL2	ENST00000513343.1 linkuse as main transcript	c.390C>T	p.Asp130=	synonymous_variant	4/5	3
ELL2	ENST00000505584.1 linkuse as main transcript	n.247C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

44043

AN:

151938

Hom.:

6531

Cov.:

show subpopulations

Gnomad AFR

AF:

0.345

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.409

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.279

GnomAD3 exomes

AF:

0.264

AC:

62323

AN:

235726

Hom.:

8727

AF XY:

0.266

AC XY:

33831

AN XY:

127250

show subpopulations

Gnomad AFR exome

AF:

0.343

Gnomad AMR exome

AF:

0.188

Gnomad ASJ exome

AF:

0.189

Gnomad EAS exome

AF:

0.400

Gnomad SAS exome

AF:

0.301

Gnomad FIN exome

AF:

0.266

Gnomad NFE exome

AF:

0.251

Gnomad OTH exome

AF:

0.240

GnomAD4 exome

AF:

0.265

AC:

377761

AN:

1426590

Hom.:

52254

Cov.:

AF XY:

0.267

AC XY:

189402

AN XY:

709860

show subpopulations

Gnomad4 AFR exome

AF:

0.338

Gnomad4 AMR exome

AF:

0.191

Gnomad4 ASJ exome

AF:

0.205

Gnomad4 EAS exome

AF:

0.351

Gnomad4 SAS exome

AF:

0.317

Gnomad4 FIN exome

AF:

0.271

Gnomad4 NFE exome

AF:

0.259

Gnomad4 OTH exome

AF:

0.279

GnomAD4 genome

AF:

0.290

AC:

44090

AN:

152056

Hom.:

6543

Cov.:

AF XY:

0.290

AC XY:

21544

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.346

Gnomad4 AMR

AF:

0.235

Gnomad4 ASJ

AF:

0.208

Gnomad4 EAS

AF:

0.408

Gnomad4 SAS

AF:

0.356

Gnomad4 FIN

AF:

0.274

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.279

Alfa

AF:

0.260

Hom.:

6225

Bravo

AF:

0.289

Asia WGS

AF:

0.373

AC:

1298

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.5

DANN

Benign

0.74

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

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