rs6837455

Positions:

• chr4-122667787-G-C

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+18076G>C 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 0.179 in 152,108 control chromosomes in the GnomAD database, including 2,726 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 0.18 (2726 hom., cov: 32)
• Consequence: IL21-AS1 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL21-AS1	NR_104126.1	n.3128+18076G>C		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+18076G>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27169 AN: 151988 Hom.: 2724 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.0667

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.179 AC: 27182 AN: 152108 Hom.: 2726 Cov.: 32 AF XY: 0.179 AC XY: 13325 AN XY: 74384

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.0667

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.164

Alfa AF: 0.157 Hom.: 243

Bravo AF: 0.187

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6837455; hg19: chr4-123588942;