11-75154795-G-T

Variant names:

• chr11-75154795-G-T
• rs4944993
• NM_007256.5:c.16+3398G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 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.16+3398G>T		intron	N/A	NP_009187.1	O94956-1
	SLCO2B1	NM_001145212.3		c.16+3398G>T		intron	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.16+3398G>T		intron	N/A	ENSP00000289575.5	O94956-1
	SLCO2B1	ENST00000530556.5	TSL:1	c.-51+2965G>T		intron	N/A	ENSP00000435384.1	A0A1B0GX35
	SLCO2B1	ENST00000534004.5	TSL:1	c.-51+2279G>T		intron	N/A	ENSP00000431192.1	A0A1B0GX35

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

African (AFR) AF: 0.231 AC: 9588 AN: 41526

American (AMR) AF: 0.373 AC: 5702 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1821 AN: 5148

South Asian (SAS) AF: 0.285 AC: 1375 AN: 4818

European-Finnish (FIN) AF: 0.197 AC: 2091 AN: 10608

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.171 AC: 11632 AN: 67998

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.177 Hom.: 1443

Bravo AF: 0.241

Asia WGS AF: 0.353 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.49
PhyloP100		0.49
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: rs4944993; hg19: chr11-74865840;