1-158177156-T-C

Position:

• chr1-158177156-T-C

Variant summary

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

The ENST00000413990.1(ELL2P1):​n.600A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 1,528,100 control chromosomes in the GnomAD database, including 282,040 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 0.65 (32879 hom., cov: 31)
  • Exomes 𝑓: 0.60 (249161 hom.)
• Consequence: ELL2P1 ENST00000413990.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84

Genes affected

ELL2P1 (HGNC:39343): (elongation factor for RNA polymerase II 2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELL2P1	ENST00000413990.1	n.600A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98821 AN: 151902 Hom.: 32832 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.624

GnomAD4 exome AF: 0.598 AC: 822986 AN: 1376078 Hom.: 249161 Cov.: 32 AF XY: 0.598 AC XY: 412187 AN XY: 689058

Gnomad4 AFR exome AF: 0.757

Gnomad4 AMR exome AF: 0.763

Gnomad4 ASJ exome AF: 0.546

Gnomad4 EAS exome AF: 0.861

Gnomad4 SAS exome AF: 0.644

Gnomad4 FIN exome AF: 0.605

Gnomad4 NFE exome AF: 0.573

Gnomad4 OTH exome AF: 0.604

GnomAD4 genome AF: 0.651 AC: 98920 AN: 152022 Hom.: 32879 Cov.: 31 AF XY: 0.654 AC XY: 48564 AN XY: 74300

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.618

Alfa AF: 0.595 Hom.: 12365

Bravo AF: 0.664

Asia WGS AF: 0.703 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.022
DANN	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3021477; hg19: chr1-158146946;