rs10518400

Variant names:

• chr4-122661271-G-A
• rs10518400
• ENST00000417927.1:n.3128+11560G>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+11560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.073 in 151,832 control chromosomes in the GnomAD database, including 454 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 0.073 (454 hom., cov: 32)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• Publications: 8 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL21-AS1	NR_104126.1	n.3128+11560G>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+11560G>A		intron_variant	Intron 10 of 10	1

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11051 AN: 151714 Hom.: 449 Cov.: 32

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.0839

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0684

Gnomad OTH AF: 0.0892

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

GnomAD4 genome AF: 0.0730 AC: 11077 AN: 151832 Hom.: 454 Cov.: 32 AF XY: 0.0748 AC XY: 5551 AN XY: 74174

African (AFR) AF: 0.0577 AC: 2385 AN: 41358

American (AMR) AF: 0.117 AC: 1783 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3468

East Asian (EAS) AF: 0.0833 AC: 431 AN: 5172

South Asian (SAS) AF: 0.0843 AC: 405 AN: 4806

European-Finnish (FIN) AF: 0.0899 AC: 944 AN: 10502

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0684 AC: 4648 AN: 67948

Other (OTH) AF: 0.0878 AC: 185 AN: 2108

Alfa AF: 0.0714 Hom.: 835

Bravo AF: 0.0774

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.49
DANN	Benign	0.44
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10518400; hg19: chr4-123582426;