ENST00000417927.1:n.3128+7665T>A

Variant names:

• chr4-122657376-T-A
• rs12511287
• ENST00000417927.1:n.3128+7665T>A

Variant summary

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

The ENST00000417927.1(IL21-AS1):​n.3128+7665T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 152,050 control chromosomes in the GnomAD database, including 19,639 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 0.46 (19639 hom., cov: 31)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 7 publications found

Genes affected

IL21-AS1 (HGNC:40299): (IL21 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL21-AS1	NR_104126.1	n.3128+7665T>A		intron_variant	Intron 10 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.3128+7665T>A		intron_variant	Intron 10 of 10	1

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69613 AN: 151934 Hom.: 19588 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.459 AC: 69718 AN: 152050 Hom.: 19639 Cov.: 31 AF XY: 0.456 AC XY: 33886 AN XY: 74358

African (AFR) AF: 0.786 AC: 32568 AN: 41438

American (AMR) AF: 0.452 AC: 6916 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1668 AN: 3468

East Asian (EAS) AF: 0.418 AC: 2165 AN: 5176

South Asian (SAS) AF: 0.537 AC: 2581 AN: 4810

European-Finnish (FIN) AF: 0.219 AC: 2317 AN: 10590

Middle Eastern (MID) AF: 0.469 AC: 136 AN: 290

European-Non Finnish (NFE) AF: 0.298 AC: 20222 AN: 67970

Other (OTH) AF: 0.444 AC: 937 AN: 2112

Alfa AF: 0.160 Hom.: 249

Bravo AF: 0.491

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.021
DANN	Benign	0.78
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12511287; hg19: chr4-123578531;