5-95899087-C-T

Variant names:

• chr5-95899087-C-T
• rs3777200
• NM_012081.6:c.955-277G>A

Variant summary

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

The NM_012081.6(ELL2):​c.955-277G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,032 control chromosomes in the GnomAD database, including 7,976 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 0.31 (7976 hom., cov: 32)
• Consequence: ELL2 NM_012081.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 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.955-277G>A		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.955-277G>A		intron	N/A	ENSP00000237853.4
	ELL2	ENST00000513343.1	TSL:3	c.409-277G>A		intron	N/A	ENSP00000423915.1
	ENSG00000250362	ENST00000718070.1		n.739+22267C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47762 AN: 151914 Hom.: 7956 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.315 AC: 47820 AN: 152032 Hom.: 7976 Cov.: 32 AF XY: 0.314 AC XY: 23327 AN XY: 74300

African (AFR) AF: 0.431 AC: 17880 AN: 41444

American (AMR) AF: 0.242 AC: 3698 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2111 AN: 5172

South Asian (SAS) AF: 0.355 AC: 1709 AN: 4810

European-Finnish (FIN) AF: 0.274 AC: 2893 AN: 10554

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17873 AN: 67988

Other (OTH) AF: 0.295 AC: 623 AN: 2112

Alfa AF: 0.289 Hom.: 10904

Bravo AF: 0.318

Asia WGS AF: 0.377 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.37
PhyloP100		-0.12
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: rs3777200; hg19: chr5-95234791;