rs6840978

Positions:

• chr4-122633552-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.2797+4556C>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 0.161 in 152,100 control chromosomes in the GnomAD database, including 2,080 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 0.16 (2080 hom., cov: 32)
• Consequence: IL21-AS1 NR_104126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL21-AS1	NR_104126.1	n.2797+4556C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL21-AS1	ENST00000417927.1	n.2797+4556C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24497 AN: 151982 Hom.: 2077 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.161 AC: 24517 AN: 152100 Hom.: 2080 Cov.: 32 AF XY: 0.157 AC XY: 11641 AN XY: 74360

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.144

Alfa AF: 0.180 Hom.: 3505

Bravo AF: 0.158

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6840978; hg19: chr4-123554707;