chr5-95899087-C-T

Position:

• chr5-95899087-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELL2	NM_012081.6	c.955-277G>A		intron_variant		ENST00000237853.9	NP_036213.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELL2	ENST00000237853.9	c.955-277G>A		intron_variant		1	NM_012081.6	ENSP00000237853.4
ELL2	ENST00000513343.1	c.409-277G>A		intron_variant		3		ENSP00000423915.1

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

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.295

Alfa AF: 0.287 Hom.: 1222

Bravo AF: 0.318

Asia WGS AF: 0.377 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.37

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: rs3777200; hg19: chr5-95234791;