chr5-95926809-C-T

Variant names:

• chr5-95926809-C-T
• rs11738945
• NM_012081.6:c.196-7264G>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.196-7264G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,002 control chromosomes in the GnomAD database, including 2,411 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 0.16 (2411 hom., cov: 31)
• Consequence: ELL2 NM_012081.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELL2	NM_012081.6	c.196-7264G>A		intron_variant	Intron 2 of 11	ENST00000237853.9	NP_036213.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELL2	ENST00000237853.9	c.196-7264G>A		intron_variant	Intron 2 of 11	1	NM_012081.6	ENSP00000237853.4

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24793 AN: 151884 Hom.: 2412 Cov.: 31

Gnomad AFR AF: 0.0596

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.163 AC: 24787 AN: 152002 Hom.: 2411 Cov.: 31 AF XY: 0.165 AC XY: 12255 AN XY: 74270

African (AFR) AF: 0.0594 AC: 2465 AN: 41496

American (AMR) AF: 0.176 AC: 2682 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 470 AN: 3472

East Asian (EAS) AF: 0.340 AC: 1760 AN: 5172

South Asian (SAS) AF: 0.190 AC: 917 AN: 4814

European-Finnish (FIN) AF: 0.211 AC: 2222 AN: 10508

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13674 AN: 67958

Other (OTH) AF: 0.175 AC: 368 AN: 2106

Alfa AF: 0.177 Hom.: 331

Bravo AF: 0.158

Asia WGS AF: 0.240 AC: 830 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.78
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: rs11738945; hg19: chr5-95262513;