rs2069824

Positions:

• chr7-22725613-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_131935.1(IL6-AS1):​n.1146A>G 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 0.0974 in 152,134 control chromosomes in the GnomAD database, including 818 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 0.097 (818 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IL6-AS1 NR_131935.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

Genes affected

IL6-AS1 (HGNC:40301): (IL6 antisense RNA 1)

STEAP1B (HGNC:41907): (STEAP family member 1B) Predicted to be integral component of membrane. Predicted to be active in endosome and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL6-AS1	NR_131935.1	n.1146A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL6-AS1	ENST00000325042.2	n.1146A>G		non_coding_transcript_exon_variant	2/2	1
STEAP1B	ENST00000650428.1	n.46+1955A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0975 AC: 14817 AN: 152016 Hom.: 819 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0823

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.0994

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.123

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 20

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0974 AC: 14822 AN: 152134 Hom.: 818 Cov.: 32 AF XY: 0.0988 AC XY: 7346 AN XY: 74376

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0822

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.000968

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0806

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0961 Hom.: 908

Bravo AF: 0.0965

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069824; hg19: chr7-22765232;