11-75154795-G-T

Position:

• chr11-75154795-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007256.5(SLCO2B1):​c.16+3398G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,176 control chromosomes in the GnomAD database, including 4,255 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 0.22 (4255 hom., cov: 32)
• Consequence: SLCO2B1 NM_007256.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

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]

SLCO2B1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO2B1	NM_007256.5	c.16+3398G>T		intron_variant		ENST00000289575.10	NP_009187.1
SLCO2B1	NM_001145212.3	c.16+3398G>T		intron_variant			NP_001138684.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO2B1	ENST00000289575.10	c.16+3398G>T		intron_variant		1	NM_007256.5	ENSP00000289575.5

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34050 AN: 152058 Hom.: 4242 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.224 AC: 34094 AN: 152176 Hom.: 4255 Cov.: 32 AF XY: 0.229 AC XY: 17029 AN XY: 74402

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.236

Alfa AF: 0.175 Hom.: 1265

Bravo AF: 0.241

Asia WGS AF: 0.353 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.49

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: rs4944993; hg19: chr11-74865840;