4-122675539-A-T

Position:

• chr4-122675539-A-T

Variant summary

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

The NR_104126.1(IL21-AS1):​n.3129-12998A>T 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 0.707 in 152,116 control chromosomes in the GnomAD database, including 40,394 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 0.71 (40394 hom., cov: 32)
• Consequence: IL21-AS1 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL21-AS1	NR_104126.1	n.3129-12998A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.3129-12998A>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107458 AN: 151998 Hom.: 40334 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.707 AC: 107576 AN: 152116 Hom.: 40394 Cov.: 32 AF XY: 0.704 AC XY: 52312 AN XY: 74326

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.701

Alfa AF: 0.625 Hom.: 3702

Bravo AF: 0.742

Asia WGS AF: 0.897 AC: 3118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6534359; hg19: chr4-123596694;