11-75170211-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO2B1	NM_007256.5	c.781+447T>C		intron_variant		ENST00000289575.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO2B1	ENST00000289575.10	c.781+447T>C		intron_variant		1	NM_007256.5	P2

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

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.281

Alfa AF: 0.224 Hom.: 3926

Bravo AF: 0.279

Asia WGS AF: 0.416 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.5
Dann	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs11236365; hg19: chr11-74881256;