5-95924158-C-T

Position:

• chr5-95924158-C-T

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.196-4613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,068 control chromosomes in the GnomAD database, including 9,225 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.33 (9225 hom., cov: 32)
• Consequence: ELL2 NM_012081.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.34

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=-0.9).
• BP6: Variant 5-95924158-C-T is Benign according to our data. Variant chr5-95924158-C-T is described in ClinVar as [Benign]. Clinvar id is 1277603.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELL2	NM_012081.6	c.196-4613G>A		intron_variant		ENST00000237853.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELL2	ENST00000237853.9	c.196-4613G>A		intron_variant		1	NM_012081.6	P1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50472 AN: 151950 Hom.: 9196 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.332 AC: 50541 AN: 152068 Hom.: 9225 Cov.: 32 AF XY: 0.331 AC XY: 24620 AN XY: 74344

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.306

Alfa AF: 0.269 Hom.: 7408

Bravo AF: 0.338

Asia WGS AF: 0.383 AC: 1331 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

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	-0.90
CADD	Benign	0.55
DANN	Benign	0.36

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: rs3777185; hg19: chr5-95259862;