rs7664318

Positions:

• chr4-122677969-A-G

Variant summary

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

The NR_104126.1(IL21-AS1):​n.3129-10568A>G 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 0.26 in 151,992 control chromosomes in the GnomAD database, including 6,901 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 0.26 (6901 hom., cov: 32)
• Consequence: IL21-AS1 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL21-AS1	NR_104126.1	n.3129-10568A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.3129-10568A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39457 AN: 151874 Hom.: 6890 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.260 AC: 39502 AN: 151992 Hom.: 6901 Cov.: 32 AF XY: 0.258 AC XY: 19151 AN XY: 74296

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.0668

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.230

Alfa AF: 0.190 Hom.: 1713

Bravo AF: 0.280

Asia WGS AF: 0.298 AC: 1038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.29
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7664318; hg19: chr4-123599124;