4-122639912-C-T

Variant names:

• chr4-122639912-C-T
• rs1512970
• ENST00000417927.1:n.2798-8189C>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.2798-8189C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,974 control chromosomes in the GnomAD database, including 4,396 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 0.22 (4396 hom., cov: 32)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 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.2798-8189C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.2798-8189C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32902 AN: 151856 Hom.: 4393 Cov.: 32

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.217 AC: 32920 AN: 151974 Hom.: 4396 Cov.: 32 AF XY: 0.220 AC XY: 16316 AN XY: 74274

African (AFR) AF: 0.0680 AC: 2818 AN: 41446

American (AMR) AF: 0.348 AC: 5315 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1778 AN: 5160

South Asian (SAS) AF: 0.390 AC: 1872 AN: 4806

European-Finnish (FIN) AF: 0.206 AC: 2170 AN: 10556

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16773 AN: 67938

Other (OTH) AF: 0.282 AC: 597 AN: 2114

Alfa AF: 0.245 Hom.: 15227

Bravo AF: 0.222

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.64
PhyloP100		0.34

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: rs1512970;

hg19: chr4-123561067;