chr11-75193317-C-A

Variant names:

• chr11-75193317-C-A
• rs1621378
• NM_007256.5:c.1175C>A

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP3

The NM_007256.5(SLCO2B1):​c.1175C>A​(p.Thr392Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 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: 33 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 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.77

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO2B1	NM_007256.5	MANE Select	c.1175C>A	p.Thr392Asn	missense	Exon 9 of 14	NP_009187.1
	SLCO2B1	NM_001145211.3		c.1109C>A	p.Thr370Asn	missense	Exon 9 of 14	NP_001138683.1
	SLCO2B1	NM_001145212.3		c.743C>A	p.Thr248Asn	missense	Exon 6 of 11	NP_001138684.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO2B1	ENST00000289575.10	TSL:1 MANE Select	c.1175C>A	p.Thr392Asn	missense	Exon 9 of 14	ENSP00000289575.5
	SLCO2B1	ENST00000428359.6	TSL:1	c.1109C>A	p.Thr370Asn	missense	Exon 9 of 14	ENSP00000388912.2
	SLCO2B1	ENST00000532236.5	TSL:2	c.827C>A	p.Thr276Asn	missense	Exon 7 of 12	ENSP00000434112.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.57
BayesDel_noAF	Benign	-0.13
CADD	Benign	19
DEOGEN2	Benign	0.11	T
LIST_S2	Uncertain	0.93	D
MetaRNN	Pathogenic	0.77	D
PhyloP100		4.6
Sift4G	Pathogenic	0.0	D
Vest4		0.75
gMVP		0.79

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: rs1621378; hg19: chr11-74904362;