rs17005931

Variant names:

• chr4-122624493-C-T
• rs17005931
• ENST00000417927.1:n.1040-177C>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.1040-177C>T variant causes a intron 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 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 10 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 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.1040-177C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.1040-177C>T		intron	N/A
	IL21-AS1	ENST00000660809.1		n.555-177C>T		intron	N/A
	IL21-AS1	ENST00000667001.1		n.551-177C>T		intron	N/A

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

African (AFR) AF: 0.127 AC: 5282 AN: 41512

American (AMR) AF: 0.352 AC: 5369 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1934 AN: 5164

South Asian (SAS) AF: 0.488 AC: 2348 AN: 4808

European-Finnish (FIN) AF: 0.255 AC: 2695 AN: 10564

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18269 AN: 67966

Other (OTH) AF: 0.295 AC: 625 AN: 2116

Alfa AF: 0.268 Hom.: 24428

Bravo AF: 0.252

Asia WGS AF: 0.418 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.041
DANN	Benign	0.56
PhyloP100		-0.79

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: rs17005931;

hg19: chr4-123545648;