rs6840978

Variant names:

• chr4-122633552-C-T
• rs6840978
• ENST00000417927.1:n.2797+4556C>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.2797+4556C>T variant causes a intron 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 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 39 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417927.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	NR_104126.1		n.2797+4556C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.2797+4556C>T		intron	N/A

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

African (AFR) AF: 0.145 AC: 6004 AN: 41496

American (AMR) AF: 0.108 AC: 1650 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3468

East Asian (EAS) AF: 0.134 AC: 692 AN: 5176

South Asian (SAS) AF: 0.148 AC: 714 AN: 4816

European-Finnish (FIN) AF: 0.119 AC: 1257 AN: 10594

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13125 AN: 67970

Other (OTH) AF: 0.144 AC: 304 AN: 2110

Alfa AF: 0.178 Hom.: 4282

Bravo AF: 0.158

Asia WGS AF: 0.156 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.67
PhyloP100		-0.42

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6840978;

hg19: chr4-123554707;