rs11578093

Variant names:

• chr1-206497321-T-G
• rs11578093
• ENST00000367119.1:n.135+273A>C

Variant summary

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

The ENST00000367119.1(IKBKE-AS1):​n.135+273A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,758 control chromosomes in the GnomAD database, including 9,643 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 0.36 (9643 hom., cov: 32)
• Consequence: IKBKE-AS1 ENST00000367119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 5 publications found

Genes affected

IKBKE-AS1 (HGNC:32061): (IKBKE antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000367119.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IKBKE-AS1	NR_172918.1		n.135+273A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IKBKE-AS1	ENST00000367119.1	TSL:2	n.135+273A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53901 AN: 151638 Hom.: 9633 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.356 AC: 53958 AN: 151758 Hom.: 9643 Cov.: 32 AF XY: 0.353 AC XY: 26211 AN XY: 74148

African (AFR) AF: 0.333 AC: 13797 AN: 41386

American (AMR) AF: 0.391 AC: 5960 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1346 AN: 3464

East Asian (EAS) AF: 0.237 AC: 1222 AN: 5164

South Asian (SAS) AF: 0.438 AC: 2108 AN: 4808

European-Finnish (FIN) AF: 0.334 AC: 3514 AN: 10530

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24811 AN: 67860

Other (OTH) AF: 0.360 AC: 760 AN: 2112

Alfa AF: 0.360 Hom.: 15601

Bravo AF: 0.356

Asia WGS AF: 0.334 AC: 1165 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11578093; hg19: chr1-206670654;