11-106070777-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_198439.3(KBTBD3):​c.-13+5730A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 152,214 control chromosomes in the GnomAD database, including 28 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 0.012 ( 28 hom., cov: 33)

Consequence

KBTBD3
NM_198439.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.400
Variant links:
Genes affected
KBTBD3 (HGNC:22934): (kelch repeat and BTB domain containing 3)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0117 (1780/152214) while in subpopulation AMR AF= 0.0196 (299/15292). AF 95% confidence interval is 0.0177. There are 28 homozygotes in gnomad4. There are 828 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 28 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KBTBD3NM_198439.3 linkc.-13+5730A>C intron_variant Intron 2 of 3 ENST00000531837.2 NP_940841.1 Q8NAB2A0A024R3B5A8K1K0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KBTBD3ENST00000531837.2 linkc.-13+5730A>C intron_variant Intron 2 of 3 1 NM_198439.3 ENSP00000432163.1 Q8NAB2

Frequencies

GnomAD3 genomes
AF:
0.0117
AC:
1779
AN:
152096
Hom.:
28
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00330
Gnomad AMI
AF:
0.0822
Gnomad AMR
AF:
0.0196
Gnomad ASJ
AF:
0.00605
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00931
Gnomad FIN
AF:
0.00283
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0167
Gnomad OTH
AF:
0.0177
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0117
AC:
1780
AN:
152214
Hom.:
28
Cov.:
33
AF XY:
0.0111
AC XY:
828
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.00329
Gnomad4 AMR
AF:
0.0196
Gnomad4 ASJ
AF:
0.00605
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00932
Gnomad4 FIN
AF:
0.00283
Gnomad4 NFE
AF:
0.0167
Gnomad4 OTH
AF:
0.0175
Alfa
AF:
0.0119
Hom.:
5
Bravo
AF:
0.0131
Asia WGS
AF:
0.00289
AC:
10
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
1.2
DANN
Benign
0.74

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11226914; hg19: chr11-105941504; API