6-32293473-CTT-TTG

Variant names:

• chr6-32293473-CTT-TTG
• NM_001286474.2:c.1192_1194delAAGinsCAA
• TSBP1 p.Lys398Gln

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001286474.2(TSBP1):​c.1192_1194delAAGinsCAA​(p.Lys398Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TSBP1 NM_001286474.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 0 publications found

Genes affected

TSBP1 (HGNC:13922): (testis expressed basic protein 1) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286474.2. 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
	TSBP1	NM_001286474.2	MANE Select	c.1192_1194delAAGinsCAA	p.Lys398Gln	missense	N/A	NP_001273403.1	A0A1U9X7D1
	TSBP1	NM_006781.5		c.1198_1200delAAGinsCAA	p.Lys400Gln	missense	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.1150_1152delAAGinsCAA	p.Lys384Gln	missense	N/A	NP_001273404.1	E9PLW3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	ENST00000533191.6	TSL:1 MANE Select	c.1192_1194delAAGinsCAA	p.Lys398Gln	missense	N/A	ENSP00000431199.1	Q5SRN2-3
	TSBP1	ENST00000442822.6	TSL:1	c.1171_1173delAAGinsCAA	p.Lys391Gln	missense	N/A	ENSP00000411164.2	C9J9T8
	TSBP1	ENST00000447241.6	TSL:5	c.1198_1200delAAGinsCAA	p.Lys400Gln	missense	N/A	ENSP00000415517.2	Q5SRN2-1

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.0020

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-32261250;