rs117124364

Variant names:

• chr21-32997453-C-T
• rs117124364
• ENST00000454622.2:n.201+73451G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000454622.2(ENSG00000227757):​n.201+73451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 152,268 control chromosomes in the GnomAD database, including 3 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 0.010 (3 hom., cov: 32)
• Consequence: ENSG00000227757 ENST00000454622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 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).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0102 (1548/152268) while in subpopulation NFE AF = 0.0164 (1114/68030). AF 95% confidence interval is 0.0156. There are 3 homozygotes in GnomAd4. There are 691 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 3 gene

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+73451G>A		intron_variant	Intron 1 of 1	2
EPCIP-AS1	ENST00000700822.1	n.487-21931C>T		intron_variant	Intron 3 of 3
EPCIP-AS1	ENST00000777210.1	n.775-14116C>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.0102 AC: 1549 AN: 152150 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00345

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.00989

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00538

Gnomad FIN AF: 0.00123

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.00861

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

GnomAD4 genome AF: 0.0102 AC: 1548 AN: 152268 Hom.: 3 Cov.: 32 AF XY: 0.00928 AC XY: 691 AN XY: 74450

African (AFR) AF: 0.00344 AC: 143 AN: 41534

American (AMR) AF: 0.00987 AC: 151 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00539 AC: 26 AN: 4828

European-Finnish (FIN) AF: 0.00123 AC: 13 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0164 AC: 1114 AN: 68030

Other (OTH) AF: 0.00852 AC: 18 AN: 2112

Alfa AF: 0.0125 Hom.: 0

Bravo AF: 0.0109

Asia WGS AF: 0.00289 AC: 10 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	1.4
DANN	Benign	0.084
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs117124364; hg19: chr21-34369761;