rs13132308

Variant names:

• chr4-122629959-A-G
• rs13132308
• ENST00000417927.1:n.2797+963A>G

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+963A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 151,912 control chromosomes in the GnomAD database, including 1,066 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 0.10 (1066 hom., cov: 32)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984
• Publications: 19 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 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+963A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.2797+963A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15860 AN: 151794 Hom.: 1066 Cov.: 32

Gnomad AFR AF: 0.0357

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0959

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.0932

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

GnomAD4 genome AF: 0.104 AC: 15862 AN: 151912 Hom.: 1066 Cov.: 32 AF XY: 0.101 AC XY: 7469 AN XY: 74216

African (AFR) AF: 0.0356 AC: 1476 AN: 41422

American (AMR) AF: 0.0768 AC: 1173 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0959 AC: 332 AN: 3462

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0884 AC: 425 AN: 4810

European-Finnish (FIN) AF: 0.107 AC: 1131 AN: 10526

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10938 AN: 67934

Other (OTH) AF: 0.0918 AC: 194 AN: 2114

Alfa AF: 0.108 Hom.: 224

Bravo AF: 0.0972

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.71
PhyloP100		-0.98

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: rs13132308;

hg19: chr4-123551114;