5-95917404-C-G

Position:

• chr5-95917404-C-G

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.317+2020G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,012 control chromosomes in the GnomAD database, including 9,562 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (9562 hom., cov: 32)
• Consequence: ELL2 NM_012081.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.226

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=-0.8).
• BP6: Variant 5-95917404-C-G is Benign according to our data. Variant chr5-95917404-C-G is described in ClinVar as [Benign]. Clinvar id is 1257675.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELL2	NM_012081.6	c.317+2020G>C		intron_variant		ENST00000237853.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELL2	ENST00000237853.9	c.317+2020G>C		intron_variant		1	NM_012081.6	P1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51201 AN: 151892 Hom.: 9537 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.337 AC: 51263 AN: 152012 Hom.: 9562 Cov.: 32 AF XY: 0.336 AC XY: 24979 AN XY: 74302

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.308

Alfa AF: 0.288 Hom.: 811

Bravo AF: 0.343

Asia WGS AF: 0.383 AC: 1333 AN: 3478

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

Jul 13, 2018

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

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.3
DANN	Benign	0.79
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3777189; hg19: chr5-95253108;