rs9307509

Variant names:

• chr4-122667336-T-A
• rs9307509
• ENST00000417927.1:n.3128+17625T>A

Your query was ambiguous. Multiple possible variants found:

• chr4-122667336-T-A
• chr4-122667336-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417927.1(IL21-AS1):​n.3128+17625T>A variant causes a intron 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 ENST00000417927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 1 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=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0992 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.3128+17625T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL21-AS1	ENST00000417927.1	TSL:1	n.3128+17625T>A		intron	N/A

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

African (AFR) AF: 0.0302 AC: 1242 AN: 41086

American (AMR) AF: 0.0758 AC: 1143 AN: 15076

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 462 AN: 3448

East Asian (EAS) AF: 0.00157 AC: 8 AN: 5086

South Asian (SAS) AF: 0.107 AC: 504 AN: 4712

European-Finnish (FIN) AF: 0.0637 AC: 671 AN: 10536

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0831 AC: 5631 AN: 67740

Other (OTH) AF: 0.0811 AC: 169 AN: 2084

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	7.0
DANN	Benign	0.81
PhyloP100		1.7

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: rs9307509;

hg19: chr4-123588491;