dbSNP rs13263558: KBTBD11:c.*70G>A (chr8-2003134-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014867.3(KBTBD11):c.*70G>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 0.000000912 in 1,097,026 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 9.1e-7 ( 0 hom. )

Consequence

KBTBD11
NM_014867.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.278

Publications

1 publications found

Variant links:

Genes affected

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

KBTBD11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
KBTBD11	NM_014867.3 link	c.*70G>A	3_prime_UTR_variant	Exon 2 of 2	ENST00000320248.4	NP_055682.1	O94819
KBTBD11	XM_011534772.3 link	c.*70G>A	3_prime_UTR_variant	Exon 3 of 3		XP_011533074.1	O94819
KBTBD11	XM_017014116.2 link	c.*70G>A	3_prime_UTR_variant	Exon 3 of 3		XP_016869605.1	O94819

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KBTBD11	ENST00000320248.4 link	c.*70G>A		3_prime_UTR_variant	Exon 2 of 2	1	NM_014867.3	ENSP00000321544.3		O94819

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

9.12e-7

AC:

AN:

1097026

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

518928

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

22772

American (AMR)

AF:

0.00

AC:

AN:

8312

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14258

East Asian (EAS)

AF:

0.00

AC:

AN:

26356

South Asian (SAS)

AF:

0.00

AC:

AN:

21344

European-Finnish (FIN)

AF:

0.00

AC:

AN:

35594

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2920

European-Non Finnish (NFE)

AF:

0.00000108

AC:

AN:

921734

Other (OTH)

AF:

0.00

AC:

AN:

43736

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

3.9

(source)

DANN

Benign

0.80

PhyloP100

-0.28

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over