rs17005931

chr4-122624493-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104126.1(IL21-AS1):n.1040-177C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,074 control chromosomes in the GnomAD database, including 5,470 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 (5470 hom., cov: 32)
• Consequence: IL21-AS1 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787

Genes affected

IL21-AS1 (HGNC:40299): (IL21 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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/exons	MANE	UniProt
IL21-AS1	NR_104126.1	n.1040-177C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.1040-177C>T		intron_variant, non_coding_transcript_variant		1
IL21-AS1	ENST00000660809.1	n.555-177C>T		intron_variant, non_coding_transcript_variant
IL21-AS1	ENST00000667001.1	n.551-177C>T		intron_variant, non_coding_transcript_variant
IL21-AS1	ENST00000668520.1	n.573-177C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38169 AN: 151954 Hom.: 5463 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.251 AC: 38199 AN: 152074 Hom.: 5470 Cov.: 32 AF XY: 0.257 AC XY: 19118 AN XY: 74310

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.295

Alfa AF: 0.276 Hom.: 12498

Bravo AF: 0.252

Asia WGS AF: 0.418 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.041
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17005931; hg19: chr4-123545648;