rs2834070

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000227757 (HGNC:):

C21orf62-AS1 (HGNC:1290): (EPCIP antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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
C21orf62-AS1	ENST00000700822.1	n.487-4240G>T		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.0569

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.265

Alfa AF: 0.314 Hom.: 10711

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2834070; hg19: chr21-34387452;