chr21-32971825-T-C

Variant names:

• chr21-32971825-T-C
• rs2834036
• ENST00000454622.2:n.202-57696A>G

Variant summary

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

The ENST00000454622.2(ENSG00000227757):​n.202-57696A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,872 control chromosomes in the GnomAD database, including 16,991 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 0.44 (16991 hom., cov: 31)
• Consequence: ENSG00000227757 ENST00000454622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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.202-57696A>G		intron_variant	Intron 1 of 1	2
EPCIP-AS1	ENST00000700822.1	n.487-47559T>C		intron_variant	Intron 3 of 3
EPCIP-AS1	ENST00000777210.1	n.775-39744T>C		intron_variant	Intron 5 of 6
EPCIP-AS1	ENST00000777211.1	n.956-9020T>C		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67338 AN: 151750 Hom.: 16965 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.444 AC: 67403 AN: 151872 Hom.: 16991 Cov.: 31 AF XY: 0.435 AC XY: 32299 AN XY: 74224

African (AFR) AF: 0.691 AC: 28595 AN: 41384

American (AMR) AF: 0.367 AC: 5599 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1555 AN: 3472

East Asian (EAS) AF: 0.0697 AC: 360 AN: 5162

South Asian (SAS) AF: 0.276 AC: 1328 AN: 4808

European-Finnish (FIN) AF: 0.354 AC: 3730 AN: 10528

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24877 AN: 67946

Other (OTH) AF: 0.414 AC: 872 AN: 2108

Alfa AF: 0.386 Hom.: 23808

Bravo AF: 0.458

Asia WGS AF: 0.210 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.88
DANN	Benign	0.44
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2834036; hg19: chr21-34344133;