chr5-95907227-T-C

Variant names:

• chr5-95907227-T-C
• rs56219066
• NM_012081.6:c.482-445A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012081.6(ELL2):​c.482-445A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 148,872 control chromosomes in the GnomAD database, including 6,832 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 0.30 (6832 hom., cov: 28)
• Consequence: ELL2 NM_012081.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563
• Publications: 19 publications found

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]

ENSG00000250362 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012081.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELL2	NM_012081.6	MANE Select	c.482-445A>G		intron	N/A	NP_036213.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELL2	ENST00000237853.9	TSL:1 MANE Select	c.482-445A>G		intron	N/A	ENSP00000237853.4
	ELL2	ENST00000513343.1	TSL:3	c.196-6147A>G		intron	N/A	ENSP00000423915.1
	ELL2	ENST00000506628.1	TSL:5	n.262-445A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.297 AC: 44202 AN: 148796 Hom.: 6823 Cov.: 28

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.297 AC: 44228 AN: 148872 Hom.: 6832 Cov.: 28 AF XY: 0.296 AC XY: 21505 AN XY: 72616

African (AFR) AF: 0.382 AC: 15208 AN: 39862

American (AMR) AF: 0.233 AC: 3489 AN: 14970

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3466

East Asian (EAS) AF: 0.406 AC: 2072 AN: 5108

South Asian (SAS) AF: 0.352 AC: 1668 AN: 4736

European-Finnish (FIN) AF: 0.254 AC: 2488 AN: 9794

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17693 AN: 67660

Other (OTH) AF: 0.284 AC: 589 AN: 2074

Alfa AF: 0.312 Hom.: 2713

Bravo AF: 0.303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.31
PhyloP100		0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs56219066; hg19: chr5-95242931;