8-2005401-C-G

Variant names:

• chr8-2005401-C-G
• rs1043225
• NM_014867.3:c.*2337C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014867.3(KBTBD11):​c.*2337C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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.

• Frequency: Genomes: not found (cov: 34)
• Consequence: KBTBD11 NM_014867.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43
• Publications: 2 publications found

Genes affected

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

ACMG classification

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=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014867.3. 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
	KBTBD11	NM_014867.3	MANE Select	c.*2337C>G		3_prime_UTR	Exon 2 of 2	NP_055682.1	O94819

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KBTBD11	ENST00000320248.4	TSL:1 MANE Select	c.*2337C>G		3_prime_UTR	Exon 2 of 2	ENSP00000321544.3	O94819
	KBTBD11	ENST00000914270.1		c.*2337C>G		3_prime_UTR	Exon 3 of 3	ENSP00000584329.1
	KBTBD11	ENST00000947466.1		c.*2337C>G		3_prime_UTR	Exon 3 of 3	ENSP00000617525.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.030
DANN	Benign	0.39
PhyloP100		-3.4

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: rs1043225; hg19: chr8-1953567;