rs3887104

Variant names:

• chr1-154404195-C-T
• rs3887104
• ENST00000424435.1:n.127-238G>A

Variant summary

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

The ENST00000424435.1(IL6R-AS1):​n.127-238G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 150,678 control chromosomes in the GnomAD database, including 1,779 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 0.15 (1779 hom., cov: 29)
• Consequence: IL6R-AS1 ENST00000424435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 8 publications found

Genes affected

IL6R-AS1 (HGNC:53716): (IL6R 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 (NFE) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL6R-AS1	NR_147855.1	n.127-238G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL6R-AS1	ENST00000424435.1	n.127-238G>A		intron_variant	Intron 1 of 1	1
IL6R-AS1	ENST00000789562.1	n.131-238G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22782 AN: 150564 Hom.: 1778 Cov.: 29

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0935

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.151 AC: 22797 AN: 150678 Hom.: 1779 Cov.: 29 AF XY: 0.151 AC XY: 11122 AN XY: 73490

African (AFR) AF: 0.128 AC: 5239 AN: 41006

American (AMR) AF: 0.124 AC: 1881 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.0935 AC: 324 AN: 3466

East Asian (EAS) AF: 0.0631 AC: 323 AN: 5116

South Asian (SAS) AF: 0.169 AC: 806 AN: 4762

European-Finnish (FIN) AF: 0.165 AC: 1679 AN: 10154

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.178 AC: 12041 AN: 67740

Other (OTH) AF: 0.152 AC: 318 AN: 2094

Alfa AF: 0.169 Hom.: 1718

Bravo AF: 0.148

Asia WGS AF: 0.127 AC: 442 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.32
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs3887104; hg19: chr1-154376671;