11-75193317-CC-TT

Variant names:

• chr11-75193317-CC-TT
• NM_007256.5:c.1175_1176delCCinsTT
• SLCO2B1 p.Thr392Ile

Variant summary

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

The NM_007256.5(SLCO2B1):​c.1175_1176delCCinsTT​(p.Thr392Ile) variant causes a missense change. 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: 32)
• Consequence: SLCO2B1 NM_007256.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.55
• Publications: 0 publications found

Genes affected

SLCO2B1 (HGNC:10962): (solute carrier organic anion transporter family member 2B1) This locus encodes a member of the organic anion-transporting polypeptide family of membrane proteins. The protein encoded by this locus may function in regulation of placental uptake of sulfated steroids. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2010]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007256.5. 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
	SLCO2B1	NM_007256.5	MANE Select	c.1175_1176delCCinsTT	p.Thr392Ile	missense	N/A	NP_009187.1	O94956-1
	SLCO2B1	NM_001145211.3		c.1109_1110delCCinsTT	p.Thr370Ile	missense	N/A	NP_001138683.1	O94956-3
	SLCO2B1	NM_001145212.3		c.743_744delCCinsTT	p.Thr248Ile	missense	N/A	NP_001138684.1	O94956-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO2B1	ENST00000289575.10	TSL:1 MANE Select	c.1175_1176delCCinsTT	p.Thr392Ile	missense	N/A	ENSP00000289575.5	O94956-1
	SLCO2B1	ENST00000428359.6	TSL:1	c.1109_1110delCCinsTT	p.Thr370Ile	missense	N/A	ENSP00000388912.2	O94956-3
	SLCO2B1	ENST00000891032.1		c.1175_1176delCCinsTT	p.Thr392Ile	missense	N/A	ENSP00000561091.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.6

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: chr11-74904362;