4-122675539-A-T

Variant names:

• chr4-122675539-A-T
• rs6534359
• ENST00000417927.1:n.3129-12998A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417927.1(IL21-AS1):​n.3129-12998A>T variant causes a intron 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 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417927.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	NR_104126.1		n.3129-12998A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.3129-12998A>T		intron	N/A

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

African (AFR) AF: 0.925 AC: 38437 AN: 41532

American (AMR) AF: 0.741 AC: 11324 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2552 AN: 3468

East Asian (EAS) AF: 0.961 AC: 4972 AN: 5174

South Asian (SAS) AF: 0.871 AC: 4189 AN: 4812

European-Finnish (FIN) AF: 0.398 AC: 4193 AN: 10548

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39578 AN: 67978

Other (OTH) AF: 0.701 AC: 1476 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs6534359; hg19: chr4-123596694;