rs2833991

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377136	XR_937669.3	n.1033-3199A>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPCIP-AS1	ENST00000454365.1	n.406-3199A>C		intron_variant	Intron 3 of 3	4
EPCIP-AS1	ENST00000650763.1	n.366-3199A>C		intron_variant	Intron 3 of 7
EPCIP-AS1	ENST00000700822.1	n.295-3199A>C		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs2833991; hg19: chr21-34262687;