rs3777193

Positions:

• chr5-95911056-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012081.6(ELL2):​c.481+2715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,952 control chromosomes in the GnomAD database, including 11,939 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 0.37 (11939 hom., cov: 32)
• Consequence: ELL2 NM_012081.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELL2	NM_012081.6	c.481+2715C>T		intron_variant		ENST00000237853.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELL2	ENST00000237853.9	c.481+2715C>T		intron_variant		1	NM_012081.6	P1
ELL2	ENST00000513343.1	c.196-9976C>T		intron_variant		3
ELL2	ENST00000506628.1	n.262-4274C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56699 AN: 151836 Hom.: 11902 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.374 AC: 56775 AN: 151952 Hom.: 11939 Cov.: 32 AF XY: 0.374 AC XY: 27785 AN XY: 74280

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.345

Alfa AF: 0.307 Hom.: 1552

Bravo AF: 0.385

Asia WGS AF: 0.443 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.39
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: rs3777193; hg19: chr5-95246760;