4-122629543-G-A

Variant names:

• chr4-122629543-G-A
• rs4833838
• ENST00000417927.1:n.2797+547G>A

Variant summary

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

The ENST00000417927.1(IL21-AS1):​n.2797+547G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.977 in 152,294 control chromosomes in the GnomAD database, including 72,745 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 0.98 (72745 hom., cov: 31)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702
• Publications: 4 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 = 0.986 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.2797+547G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.2797+547G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.977 AC: 148723 AN: 152176 Hom.: 72685 Cov.: 31

Gnomad AFR AF: 0.994

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.988

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.965

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.984

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

GnomAD4 genome AF: 0.977 AC: 148842 AN: 152294 Hom.: 72745 Cov.: 31 AF XY: 0.979 AC XY: 72881 AN XY: 74458

African (AFR) AF: 0.994 AC: 41310 AN: 41564

American (AMR) AF: 0.988 AC: 15096 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.994 AC: 3450 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5180 AN: 5180

South Asian (SAS) AF: 0.996 AC: 4807 AN: 4824

European-Finnish (FIN) AF: 0.965 AC: 10247 AN: 10618

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.962 AC: 65465 AN: 68030

Other (OTH) AF: 0.984 AC: 2083 AN: 2116

Alfa AF: 0.968 Hom.: 141292

Bravo AF: 0.980

Asia WGS AF: 0.997 AC: 3468 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	0.14
DANN	Benign	0.63
PhyloP100		-0.70

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: rs4833838;

hg19: chr4-123550698;