rs10518400

Positions:

• chr4-122661271-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104126.1(IL21-AS1):​n.3128+11560G>A variant causes a intron, non coding transcript 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 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
IL21-AS1	NR_104126.1	n.3128+11560G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.3128+11560G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0577

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.0833

Gnomad4 SAS AF: 0.0843

Gnomad4 FIN AF: 0.0899

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.0878

Alfa AF: 0.0699 Hom.: 565

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518400; hg19: chr4-123582426;