rs9307509

chr4-122667336-T-Achr4-122667336-T-C

Variant summary

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

The NR_104126.1(IL21-AS1):n.3128+17625T>A 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 0.066 in 150,972 control chromosomes in the GnomAD database, including 432 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 0.066 (432 hom., cov: 32)
• Consequence: IL21-AS1 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

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=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL21-AS1	NR_104126.1	n.3128+17625T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.3128+17625T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0660 AC: 9963 AN: 150854 Hom.: 433 Cov.: 32

Gnomad AFR AF: 0.0303

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.00157

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0637

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0831

Gnomad OTH AF: 0.0820

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

GnomAD4 genome AF: 0.0660 AC: 9961 AN: 150972 Hom.: 432 Cov.: 32 AF XY: 0.0655 AC XY: 4829 AN XY: 73712

Gnomad4 AFR AF: 0.0302

Gnomad4 AMR AF: 0.0758

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.00157

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0637

Gnomad4 NFE AF: 0.0831

Gnomad4 OTH AF: 0.0811

Alfa AF: 0.0168 Hom.: 7

Bravo AF: 0.0644

Asia WGS AF: 0.0490 AC: 172 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	7.0
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9307509; hg19: chr4-123588491;