8-1808419-G-A

Position:

• chr8-1808419-G-A

Variant summary

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

The ENST00000635855.1(KBTBD11-OT1):​n.544-34934G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,664 control chromosomes in the GnomAD database, including 26,676 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 0.59 (26676 hom., cov: 31)
• Consequence: KBTBD11-OT1 ENST00000635855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

Genes affected

KBTBD11-OT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1808419G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KBTBD11-OT1	ENST00000635855.1	n.544-34934G>A		intron_variant		5		ENSP00000489726.1
KBTBD11-OT1	ENST00000635773.1	n.495+36822G>A		intron_variant		5		ENSP00000490620.1
KBTBD11-OT1	ENST00000636175.1	n.343-34934G>A		intron_variant		5		ENSP00000490769.1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89711 AN: 151546 Hom.: 26659 Cov.: 31

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.592 AC: 89777 AN: 151664 Hom.: 26676 Cov.: 31 AF XY: 0.589 AC XY: 43676 AN XY: 74098

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.627

Alfa AF: 0.594 Hom.: 39040

Bravo AF: 0.591

Asia WGS AF: 0.601 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6558545; hg19: chr8-1756585;