chr8-1805331-A-C

Position:

• chr8-1805331-A-C

Variant summary

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

The ENST00000635855.1(KBTBD11-OT1):​n.543+33734A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 151,660 control chromosomes in the GnomAD database, including 47,439 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 0.79 (47439 hom., cov: 29)
• Consequence: KBTBD11-OT1 ENST00000635855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12

Genes affected

KBTBD11-OT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1805331A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KBTBD11-OT1	ENST00000635855.1	n.543+33734A>C		intron_variant		5		ENSP00000489726.1
KBTBD11-OT1	ENST00000635773.1	n.495+33734A>C		intron_variant		5		ENSP00000490620.1
KBTBD11-OT1	ENST00000636175.1	n.342+33734A>C		intron_variant		5		ENSP00000490769.1

Frequencies

GnomAD3 genomes AF: 0.790 AC: 119660 AN: 151542 Hom.: 47384 Cov.: 29

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.790 AC: 119768 AN: 151660 Hom.: 47439 Cov.: 29 AF XY: 0.789 AC XY: 58489 AN XY: 74094

Gnomad4 AFR AF: 0.831

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.799

Alfa AF: 0.767 Hom.: 32152

Bravo AF: 0.782

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.15
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4327894; hg19: chr8-1753497;