4-122623509-C-T

Variant names:

• chr4-122623509-C-T
• rs12508721
• ENST00000417927.1:n.1040-1161C>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.1040-1161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,742 control chromosomes in the GnomAD database, including 5,469 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 0.25 (5469 hom., cov: 31)
• Consequence: IL21-AS1 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 25 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL21-AS1	NR_104126.1	n.1040-1161C>T		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.1040-1161C>T		intron_variant	Intron 4 of 10	1
IL21-AS1	ENST00000660809.1	n.555-1161C>T		intron_variant	Intron 4 of 5
IL21-AS1	ENST00000667001.1	n.551-1161C>T		intron_variant	Intron 4 of 5
IL21-AS1	ENST00000668520.1	n.573-1161C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38137 AN: 151624 Hom.: 5462 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.252 AC: 38166 AN: 151742 Hom.: 5469 Cov.: 31 AF XY: 0.258 AC XY: 19098 AN XY: 74120

African (AFR) AF: 0.128 AC: 5283 AN: 41384

American (AMR) AF: 0.351 AC: 5343 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1176 AN: 3462

East Asian (EAS) AF: 0.379 AC: 1951 AN: 5150

South Asian (SAS) AF: 0.489 AC: 2348 AN: 4804

European-Finnish (FIN) AF: 0.255 AC: 2682 AN: 10518

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18274 AN: 67912

Other (OTH) AF: 0.296 AC: 622 AN: 2102

Alfa AF: 0.261 Hom.: 780

Bravo AF: 0.253

Asia WGS AF: 0.418 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.69
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs12508721; hg19: chr4-123544664;