chr4-122626386-C-T

Variant names:

• chr4-122626386-C-T
• rs4295278
• ENST00000417927.1:n.2258C>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.2258C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.967 in 152,262 control chromosomes in the GnomAD database, including 71,148 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 0.97 (71134 hom., cov: 30)
  • Exomes 𝑓: 1.0 (14 hom.)
• Consequence: IL21-AS1 ENST00000417927.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL21-AS1	NR_104126.1	n.2258C>T		non_coding_transcript_exon_variant	Exon 6 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.2258C>T		non_coding_transcript_exon_variant	Exon 6 of 11	1
IL21-AS1	ENST00000668520.1	n.670-282C>T		intron_variant	Intron 6 of 6
IL21-AS1	ENST00000660809.1	n.*159C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.966 AC: 147016 AN: 152116 Hom.: 71074 Cov.: 30

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.972

GnomAD4 exome AF: 1.00 AC: 28 AN: 28 Hom.: 14 Cov.: 0 AF XY: 1.00 AC XY: 22 AN XY: 22

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 26 AN: 26

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.967 AC: 147135 AN: 152234 Hom.: 71134 Cov.: 30 AF XY: 0.968 AC XY: 72067 AN XY: 74428

African (AFR) AF: 0.991 AC: 41169 AN: 41532

American (AMR) AF: 0.978 AC: 14966 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3429 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5152 AN: 5152

South Asian (SAS) AF: 0.996 AC: 4807 AN: 4826

European-Finnish (FIN) AF: 0.952 AC: 10100 AN: 10612

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64268 AN: 68018

Other (OTH) AF: 0.972 AC: 2053 AN: 2112

Alfa AF: 0.953 Hom.: 132886

Bravo AF: 0.970

Asia WGS AF: 0.997 AC: 3463 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.55
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs4295278; hg19: chr4-123547541;