rs2834070

Variant names:

• chr21-33015144-G-T
• rs2834070
• ENST00000454622.2:n.201+55760C>A

Variant summary

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

The ENST00000454622.2(ENSG00000227757):​n.201+55760C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,182 control chromosomes in the GnomAD database, including 5,255 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 0.24 (5255 hom., cov: 33)
• Consequence: ENSG00000227757 ENST00000454622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 11 publications found

Genes affected

ENSG00000227757 (HGNC:):

EPCIP-AS1 (HGNC:1290): (EPCIP antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227757	ENST00000454622.2	n.201+55760C>A		intron_variant	Intron 1 of 1	2
EPCIP-AS1	ENST00000700822.1	n.487-4240G>T		intron_variant	Intron 3 of 3
ENSG00000227757	ENST00000777421.1	n.92-33481C>A		intron_variant	Intron 1 of 1
ENSG00000227757	ENST00000777423.1	n.114+11044C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37150 AN: 152064 Hom.: 5256 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.244 AC: 37155 AN: 152182 Hom.: 5255 Cov.: 33 AF XY: 0.242 AC XY: 17973 AN XY: 74392

African (AFR) AF: 0.123 AC: 5124 AN: 41522

American (AMR) AF: 0.209 AC: 3201 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3470

East Asian (EAS) AF: 0.0569 AC: 295 AN: 5184

South Asian (SAS) AF: 0.273 AC: 1314 AN: 4822

European-Finnish (FIN) AF: 0.294 AC: 3119 AN: 10594

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22251 AN: 67976

Other (OTH) AF: 0.265 AC: 559 AN: 2112

Alfa AF: 0.302 Hom.: 13943

Bravo AF: 0.233

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs2834070; hg19: chr21-34387452;