rs7700895

Variant names:

• chr5-95937706-T-A
• rs7700895
• NM_012081.6:c.195+5296A>T

Variant summary

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

The NM_012081.6(ELL2):​c.195+5296A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,996 control chromosomes in the GnomAD database, including 9,561 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 0.33 (9561 hom., cov: 32)
• Consequence: ELL2 NM_012081.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.786

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=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELL2	NM_012081.6	c.195+5296A>T		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.195+5296A>T		intron_variant	Intron 2 of 11	1	NM_012081.6	ENSP00000237853.4

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49552 AN: 151878 Hom.: 9524 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.327 AC: 49631 AN: 151996 Hom.: 9561 Cov.: 32 AF XY: 0.327 AC XY: 24327 AN XY: 74306

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.295

Alfa AF: 0.277 Hom.: 820

Bravo AF: 0.341

Asia WGS AF: 0.372 AC: 1292 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.1
DANN	Benign	0.58

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: rs7700895; hg19: chr5-95273410;