rs6558545

Variant names:

• chr8-1808419-G-A
• rs6558545
• ENST00000635855.1:n.544-34934G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-1808419-G-A
• chr8-1808419-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

KBTBD11-OT1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KBTBD11-OT1	ENST00000635855.1	n.544-34934G>A		intron_variant	Intron 2 of 29	5		ENSP00000489726.1
KBTBD11-OT1	ENST00000635773.1	n.495+36822G>A		intron_variant	Intron 1 of 27	5		ENSP00000490620.1
KBTBD11-OT1	ENST00000636175.1	n.343-34934G>A		intron_variant	Intron 1 of 6	5		ENSP00000490769.1
ENSG00000287464	ENST00000822401.1	n.421+3231C>T		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.568 AC: 23428 AN: 41254

American (AMR) AF: 0.574 AC: 8757 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2130 AN: 3472

East Asian (EAS) AF: 0.711 AC: 3664 AN: 5150

South Asian (SAS) AF: 0.556 AC: 2672 AN: 4802

European-Finnish (FIN) AF: 0.593 AC: 6227 AN: 10494

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40826 AN: 67922

Other (OTH) AF: 0.627 AC: 1325 AN: 2114

Alfa AF: 0.594 Hom.: 70140

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6558545; hg19: chr8-1756585;