4-122637099-T-G

Position:

• chr4-122637099-T-G

Variant summary

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

The NR_104126.1(IL21-AS1):​n.2797+8103T>G 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 0.467 in 151,994 control chromosomes in the GnomAD database, including 18,061 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 0.47 (18061 hom., cov: 32)
• Consequence: IL21-AS1 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL21-AS1	NR_104126.1	n.2797+8103T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.2797+8103T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71026 AN: 151878 Hom.: 18063 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.467 AC: 71038 AN: 151994 Hom.: 18061 Cov.: 32 AF XY: 0.461 AC XY: 34266 AN XY: 74306

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.475

Alfa AF: 0.559 Hom.: 33449

Bravo AF: 0.448

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2137497; hg19: chr4-123558254;