1-158177156-T-C

Variant names:

• chr1-158177156-T-C
• rs3021477
• ENST00000413990.1:n.600A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ELL2P1		n.158177156T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELL2P1	ENST00000413990.1	n.600A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.757 AC: 23945 AN: 31642

American (AMR) AF: 0.763 AC: 34051 AN: 44610

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 14009 AN: 25644

East Asian (EAS) AF: 0.861 AC: 33828 AN: 39296

South Asian (SAS) AF: 0.644 AC: 54457 AN: 84518

European-Finnish (FIN) AF: 0.605 AC: 32281 AN: 53376

Middle Eastern (MID) AF: 0.600 AC: 3368 AN: 5614

European-Non Finnish (NFE) AF: 0.573 AC: 592258 AN: 1033822

Other (OTH) AF: 0.604 AC: 34789 AN: 57556

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

African (AFR) AF: 0.754 AC: 31256 AN: 41462

American (AMR) AF: 0.713 AC: 10904 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1930 AN: 3470

East Asian (EAS) AF: 0.850 AC: 4386 AN: 5162

South Asian (SAS) AF: 0.652 AC: 3139 AN: 4814

European-Finnish (FIN) AF: 0.620 AC: 6542 AN: 10556

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.572 AC: 38844 AN: 67964

Other (OTH) AF: 0.618 AC: 1303 AN: 2108

Alfa AF: 0.598 Hom.: 17930

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
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs3021477; hg19: chr1-158146946;