1-206497321-T-G

Position:

• chr1-206497321-T-G

Variant summary

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

The NR_172918.1(IKBKE-AS1):​n.135+273A>C variant causes a intron, non coding transcript 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 NR_172918.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IKBKE-AS1	NR_172918.1	n.135+273A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IKBKE-AS1	ENST00000367119.1	n.135+273A>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.360

Alfa AF: 0.364 Hom.: 2381

Bravo AF: 0.356

Asia WGS AF: 0.334 AC: 1165 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11578093; hg19: chr1-206670654;