chr5-95929852-G-A

Position:

• chr5-95929852-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_012081.6(ELL2):​c.196-10307C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,256 control chromosomes in the GnomAD database, including 12,278 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.38 (12278 hom., cov: 30)
• Consequence: ELL2 NM_012081.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.49

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 5-95929852-G-A is Benign according to our data. Variant chr5-95929852-G-A is described in ClinVar as [Benign]. Clinvar id is 1289561.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELL2	NM_012081.6	c.196-10307C>T		intron_variant		ENST00000237853.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELL2	ENST00000237853.9	c.196-10307C>T		intron_variant		1	NM_012081.6	P1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57174 AN: 151152 Hom.: 12241 Cov.: 30

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.346

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.379 AC: 57253 AN: 151256 Hom.: 12278 Cov.: 30 AF XY: 0.379 AC XY: 27995 AN XY: 73904

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.347

Alfa AF: 0.326 Hom.: 1098

Bravo AF: 0.390

Asia WGS AF: 0.444 AC: 1542 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 09, 2019

This variant is associated with the following publications: (PMID: 29695719) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.3
DANN	Benign	0.34

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

Other links and lift over

dbSNP: rs4563648; hg19: chr5-95265556;