11-75170211-T-C

Variant names:

• chr11-75170211-T-C
• rs11236365
• NM_007256.5:c.781+447T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007256.5(SLCO2B1):​c.781+447T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,054 control chromosomes in the GnomAD database, including 5,641 homozygotes. 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: 𝑓 0.26 (5641 hom., cov: 32)
• Consequence: SLCO2B1 NM_007256.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 6 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

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.781+447T>C		intron	N/A	NP_009187.1
	SLCO2B1	NM_001145211.3		c.715+447T>C		intron	N/A	NP_001138683.1
	SLCO2B1	NM_001145212.3		c.349+447T>C		intron	N/A	NP_001138684.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO2B1	ENST00000289575.10	TSL:1 MANE Select	c.781+447T>C		intron	N/A	ENSP00000289575.5
	SLCO2B1	ENST00000428359.6	TSL:1	c.715+447T>C		intron	N/A	ENSP00000388912.2
	SLCO2B1	ENST00000891032.1		c.781+447T>C		intron	N/A	ENSP00000561091.1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39910 AN: 151936 Hom.: 5624 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.263 AC: 39971 AN: 152054 Hom.: 5641 Cov.: 32 AF XY: 0.266 AC XY: 19798 AN XY: 74320

African (AFR) AF: 0.308 AC: 12766 AN: 41474

American (AMR) AF: 0.386 AC: 5904 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1157 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1732 AN: 5166

South Asian (SAS) AF: 0.337 AC: 1618 AN: 4806

European-Finnish (FIN) AF: 0.213 AC: 2257 AN: 10578

Middle Eastern (MID) AF: 0.297 AC: 86 AN: 290

European-Non Finnish (NFE) AF: 0.201 AC: 13660 AN: 67976

Other (OTH) AF: 0.281 AC: 591 AN: 2106

Alfa AF: 0.232 Hom.: 5670

Bravo AF: 0.279

Asia WGS AF: 0.416 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.47
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs11236365; hg19: chr11-74881256;