rs2180

Variant names:

• chr21-32971971-G-A
• rs2180
• ENST00000454622.2:n.202-57842C>T

Variant summary

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

The ENST00000454622.2(ENSG00000227757):​n.202-57842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,116 control chromosomes in the GnomAD database, including 4,282 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 0.23 (4282 hom., cov: 32)
• Consequence: ENSG00000227757 ENST00000454622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454622.2. 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
	ENSG00000227757	ENST00000454622.2	TSL:2	n.202-57842C>T		intron	N/A
	EPCIP-AS1	ENST00000700822.1		n.487-47413G>A		intron	N/A
	EPCIP-AS1	ENST00000777210.1		n.775-39598G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35444 AN: 151998 Hom.: 4283 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.233 AC: 35458 AN: 152116 Hom.: 4282 Cov.: 32 AF XY: 0.230 AC XY: 17114 AN XY: 74372

African (AFR) AF: 0.200 AC: 8316 AN: 41504

American (AMR) AF: 0.254 AC: 3888 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1211 AN: 3472

East Asian (EAS) AF: 0.0604 AC: 313 AN: 5182

South Asian (SAS) AF: 0.201 AC: 967 AN: 4820

European-Finnish (FIN) AF: 0.218 AC: 2304 AN: 10570

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.258 AC: 17548 AN: 67972

Other (OTH) AF: 0.250 AC: 527 AN: 2110

Alfa AF: 0.252 Hom.: 6549

Bravo AF: 0.237

Asia WGS AF: 0.126 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.23
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: rs2180; hg19: chr21-34344279;