rs6558550

Variant names:

• chr8-1819838-A-G
• rs6558550
• ENST00000635855.1:n.544-23515A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-1819838-A-G
• chr8-1819838-A-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.544-23515A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,154 control chromosomes in the GnomAD database, including 5,894 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 0.28 (5894 hom., cov: 33)
• Consequence: KBTBD11-OT1 ENST00000635855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.48
• Publications: 8 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635855.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KBTBD11-OT1	ENST00000635855.1	TSL:5	n.544-23515A>G		intron	N/A	ENSP00000489726.1
	KBTBD11-OT1	ENST00000635773.1	TSL:5	n.496-38122A>G		intron	N/A	ENSP00000490620.1
	KBTBD11-OT1	ENST00000636175.1	TSL:5	n.343-23515A>G		intron	N/A	ENSP00000490769.1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42153 AN: 152036 Hom.: 5887 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.277 AC: 42174 AN: 152154 Hom.: 5894 Cov.: 33 AF XY: 0.277 AC XY: 20586 AN XY: 74414

African (AFR) AF: 0.289 AC: 11974 AN: 41504

American (AMR) AF: 0.306 AC: 4677 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1052 AN: 3472

East Asian (EAS) AF: 0.168 AC: 867 AN: 5172

South Asian (SAS) AF: 0.271 AC: 1307 AN: 4828

European-Finnish (FIN) AF: 0.268 AC: 2837 AN: 10594

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18603 AN: 67984

Other (OTH) AF: 0.266 AC: 562 AN: 2114

Alfa AF: 0.275 Hom.: 17065

Bravo AF: 0.280

Asia WGS AF: 0.206 AC: 719 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	0.16
DANN	Benign	0.29
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs6558550; hg19: chr8-1768004;