4-122642964-T-C

Variant names:

• chr4-122642964-T-C
• rs6419221
• ENST00000417927.1:n.2798-5137T>C

Variant summary

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

The ENST00000417927.1(IL21-AS1):​n.2798-5137T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 152,082 control chromosomes in the GnomAD database, including 32,299 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 0.65 (32299 hom., cov: 32)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 9 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.751 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.2798-5137T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.2798-5137T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98671 AN: 151964 Hom.: 32276 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.649 AC: 98729 AN: 152082 Hom.: 32299 Cov.: 32 AF XY: 0.659 AC XY: 48957 AN XY: 74326

African (AFR) AF: 0.613 AC: 25403 AN: 41468

American (AMR) AF: 0.686 AC: 10486 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2315 AN: 3468

East Asian (EAS) AF: 0.771 AC: 3985 AN: 5168

South Asian (SAS) AF: 0.772 AC: 3721 AN: 4820

European-Finnish (FIN) AF: 0.734 AC: 7754 AN: 10566

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42767 AN: 67990

Other (OTH) AF: 0.678 AC: 1431 AN: 2112

Alfa AF: 0.634 Hom.: 65190

Bravo AF: 0.642

Asia WGS AF: 0.735 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.72
PhyloP100		-0.84

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6419221;

hg19: chr4-123564119;