rs1570699

Variant names:

• chr1-158175439-T-C
• rs1570699

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.121 in 152,272 control chromosomes in the GnomAD database, including 1,553 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 0.12 (1553 hom., cov: 33)
• Consequence: ELL2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 4 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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18360 AN: 152154 Hom.: 1546 Cov.: 33

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0971

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.121 AC: 18389 AN: 152272 Hom.: 1553 Cov.: 33 AF XY: 0.127 AC XY: 9439 AN XY: 74454

African (AFR) AF: 0.0932 AC: 3875 AN: 41560

American (AMR) AF: 0.0973 AC: 1488 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 522 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2228 AN: 5176

South Asian (SAS) AF: 0.319 AC: 1539 AN: 4822

European-Finnish (FIN) AF: 0.123 AC: 1307 AN: 10602

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7180 AN: 68026

Other (OTH) AF: 0.0979 AC: 207 AN: 2114

Alfa AF: 0.103 Hom.: 155

Bravo AF: 0.115

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	11
DANN	Benign	0.55
PhyloP100		1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1570699;

hg19: chr1-158145229;