1-154402801-A-G

Variant names:

• chr1-154402801-A-G
• rs4845615
• ENST00000424435.1:n.1283T>C

Variant summary

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

The ENST00000424435.1(IL6R-AS1):​n.1283T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.975 in 152,356 control chromosomes in the GnomAD database, including 72,586 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 0.98 (72572 hom., cov: 33)
  • Exomes 𝑓: 1.0 (14 hom.)
• Consequence: IL6R-AS1 ENST00000424435.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL6R-AS1	NR_147855.1	n.1283T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL6R-AS1	ENST00000424435.1	n.1283T>C		non_coding_transcript_exon_variant	Exon 2 of 2	1
IL6R-AS1	ENST00000789562.1	n.*131T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.976 AC: 148486 AN: 152210 Hom.: 72533 Cov.: 33

Gnomad AFR AF: 0.914

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.993

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.984

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.987

GnomAD4 exome AF: 1.00 AC: 28 AN: 28 Hom.: 14 Cov.: 0 AF XY: 1.00 AC XY: 24 AN XY: 24

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 6 AN: 6

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 1.00 AC: 18 AN: 18

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.975 AC: 148583 AN: 152328 Hom.: 72572 Cov.: 33 AF XY: 0.977 AC XY: 72748 AN XY: 74488

African (AFR) AF: 0.914 AC: 37957 AN: 41548

American (AMR) AF: 0.993 AC: 15199 AN: 15306

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5190 AN: 5190

South Asian (SAS) AF: 0.999 AC: 4820 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10628 AN: 10628

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68032 AN: 68042

Other (OTH) AF: 0.987 AC: 2084 AN: 2112

Alfa AF: 0.985 Hom.: 20734

Bravo AF: 0.973

Asia WGS AF: 0.991 AC: 3448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.76
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4845615; hg19: chr1-154375277;