chr8-1970186-G-T

Variant names:

• chr8-1970186-G-T
• rs6558568
• ENST00000832959.1:n.194-1155G>T

Variant summary

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

The ENST00000832959.1(KBTBD11-OT1):​n.194-1155G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,938 control chromosomes in the GnomAD database, including 8,772 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 0.32 (8772 hom., cov: 31)
• Consequence: KBTBD11-OT1 ENST00000832959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 3 publications found

Genes affected

KBTBD11-OT1 (HGNC:49147): (KBTBD11 overlapping transcript 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832959.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KBTBD11-OT1	ENST00000832959.1		n.194-1155G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49144 AN: 151820 Hom.: 8750 Cov.: 31

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.324 AC: 49218 AN: 151938 Hom.: 8772 Cov.: 31 AF XY: 0.317 AC XY: 23573 AN XY: 74274

African (AFR) AF: 0.467 AC: 19342 AN: 41386

American (AMR) AF: 0.359 AC: 5479 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3468

East Asian (EAS) AF: 0.0675 AC: 350 AN: 5186

South Asian (SAS) AF: 0.237 AC: 1136 AN: 4802

European-Finnish (FIN) AF: 0.184 AC: 1936 AN: 10544

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19145 AN: 67966

Other (OTH) AF: 0.293 AC: 617 AN: 2104

Alfa AF: 0.294 Hom.: 15024

Bravo AF: 0.342

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		-0.076

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6558568;

hg19: chr8-1918352;