rs1043225

Positions:

• chr8-2005401-C-A
• chr8-2005401-C-G
• chr8-2005401-C-T

Variant summary

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

The NM_014867.3(KBTBD11):​c.*2337C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 167,110 control chromosomes in the GnomAD database, including 53,099 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 (47897 hom., cov: 34)
  • Exomes 𝑓: 0.84 (5202 hom.)
• Consequence: KBTBD11 NM_014867.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43

Genes affected

KBTBD11 (HGNC:29104): (kelch repeat and BTB domain containing 11)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KBTBD11	NM_014867.3	c.*2337C>A		3_prime_UTR_variant	2/2	ENST00000320248.4
KBTBD11	XM_011534772.3	c.*2337C>A		3_prime_UTR_variant	3/3
KBTBD11	XM_017014116.2	c.*2337C>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KBTBD11	ENST00000320248.4	c.*2337C>A		3_prime_UTR_variant	2/2	1	NM_014867.3	P1

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120380 AN: 152122 Hom.: 47869 Cov.: 34

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.787

GnomAD4 exome AF: 0.836 AC: 12438 AN: 14870 Hom.: 5202 Cov.: 0 AF XY: 0.831 AC XY: 5866 AN XY: 7056

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.837

Gnomad4 NFE exome AF: 0.815

Gnomad4 OTH exome AF: 0.800

GnomAD4 genome AF: 0.791 AC: 120469 AN: 152240 Hom.: 47897 Cov.: 34 AF XY: 0.798 AC XY: 59417 AN XY: 74424

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.907

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.789

Alfa AF: 0.774 Hom.: 64412

Bravo AF: 0.786

Asia WGS AF: 0.935 AC: 3253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.028
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1043225; hg19: chr8-1953567;