rs13147359

Variant names:

• chr4-122676016-T-C
• rs13147359
• ENST00000417927.1:n.3129-12521T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000417927.1(IL21-AS1):​n.3129-12521T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0232 in 152,258 control chromosomes in the GnomAD database, including 64 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 0.023 (64 hom., cov: 32)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890
• Publications: 1 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).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0232 (3531/152258) while in subpopulation NFE AF = 0.039 (2650/68020). AF 95% confidence interval is 0.0377. There are 64 homozygotes in GnomAd4. There are 1623 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 64 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL21-AS1	NR_104126.1	n.3129-12521T>C		intron_variant	Intron 10 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.3129-12521T>C		intron_variant	Intron 10 of 10	1

Frequencies

GnomAD3 genomes AF: 0.0232 AC: 3532 AN: 152140 Hom.: 64 Cov.: 32

Gnomad AFR AF: 0.00550

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0123

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00954

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0232 AC: 3531 AN: 152258 Hom.: 64 Cov.: 32 AF XY: 0.0218 AC XY: 1623 AN XY: 74442

African (AFR) AF: 0.00549 AC: 228 AN: 41558

American (AMR) AF: 0.0123 AC: 188 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00691 AC: 24 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.00934 AC: 45 AN: 4816

European-Finnish (FIN) AF: 0.0293 AC: 310 AN: 10598

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0390 AC: 2650 AN: 68020

Other (OTH) AF: 0.0156 AC: 33 AN: 2112

Alfa AF: 0.0350 Hom.: 155

Bravo AF: 0.0200

Asia WGS AF: 0.00578 AC: 20 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.73
PhyloP100		-0.89
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs13147359; hg19: chr4-123597171;