rs1282455395

Variant names:

• chr11-106053179-C-A
• rs1282455395
• NM_198439.3:c.1510G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-106053179-C-A
• chr11-106053179-C-G
• chr11-106053179-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_198439.3(KBTBD3):​c.1510G>T​(p.Ala504Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A504T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KBTBD3 NM_198439.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.72
• Publications: 0 publications found

Genes affected

KBTBD3 (HGNC:22934): (kelch repeat and BTB domain containing 3)

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.33415043).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198439.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KBTBD3	NM_198439.3	MANE Select	c.1510G>T	p.Ala504Ser	missense	Exon 4 of 4	NP_940841.1	Q8NAB2
	KBTBD3	NM_152433.4		c.1510G>T	p.Ala504Ser	missense	Exon 3 of 3	NP_689646.2
	KBTBD3	NM_001330359.2		c.1273G>T	p.Ala425Ser	missense	Exon 3 of 3	NP_001317288.1	G3V161

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KBTBD3	ENST00000531837.2	TSL:1 MANE Select	c.1510G>T	p.Ala504Ser	missense	Exon 4 of 4	ENSP00000432163.1	Q8NAB2
	KBTBD3	ENST00000526793.5	TSL:1	c.1510G>T	p.Ala504Ser	missense	Exon 3 of 3	ENSP00000436262.1	Q8NAB2
	KBTBD3	ENST00000883713.1		c.1510G>T	p.Ala504Ser	missense	Exon 4 of 4	ENSP00000553772.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Uncertain	0.13	D
BayesDel_noAF	Uncertain	-0.050
CADD	Uncertain	23
DANN	Uncertain	0.98
Eigen	Uncertain	0.36
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.86	D
M_CAP	Benign	0.043	D
MetaRNN	Benign	0.33	T
MetaSVM	Benign	-0.79	T
PhyloP100		5.7
PrimateAI	Uncertain	0.79	T
PROVEAN	Benign	-0.82	N
REVEL	Uncertain	0.33
Sift	Benign	0.41	T
Sift4G	Benign	0.18	T
Vest4		0.44
MVP		0.80
MPC		0.43
ClinPred		0.85	D
GERP RS		6.0
gMVP		0.56
Mutation Taster		=78/22	polymorphism

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

Other links and lift over

dbSNP: rs1282455395; hg19: chr11-105923906;