chr21-32890379-A-C

Variant names:

• chr21-32890379-A-C
• rs2833991
• ENST00000454365.1:n.406-3199A>C

Variant summary

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

The ENST00000454365.1(EPCIP-AS1):​n.406-3199A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 152,284 control chromosomes in the GnomAD database, including 356 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 0.056 (356 hom., cov: 32)
• Consequence: EPCIP-AS1 ENST00000454365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 2 publications found

Genes affected

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

LOC105377136 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454365.1. You can select a different transcript below to see updated ACMG assignments.

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
	EPCIP-AS1	ENST00000454365.1	TSL:4	n.406-3199A>C		intron	N/A
	EPCIP-AS1	ENST00000650763.1		n.366-3199A>C		intron	N/A
	EPCIP-AS1	ENST00000700822.1		n.295-3199A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8492 AN: 152166 Hom.: 356 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.00715

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0341

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0558 AC: 8501 AN: 152284 Hom.: 356 Cov.: 32 AF XY: 0.0545 AC XY: 4060 AN XY: 74460

African (AFR) AF: 0.111 AC: 4627 AN: 41536

American (AMR) AF: 0.0570 AC: 873 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.0560 AC: 270 AN: 4822

European-Finnish (FIN) AF: 0.00715 AC: 76 AN: 10626

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0341 AC: 2318 AN: 68014

Other (OTH) AF: 0.0752 AC: 159 AN: 2114

Alfa AF: 0.0580 Hom.: 266

Bravo AF: 0.0618

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.21
PhyloP100		-0.48

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: rs2833991;

hg19: chr21-34262687;