11-75196376-G-T

Variant names:

• chr11-75196376-G-T
• rs2306167
• NM_007256.5:c.1434-138G>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.1434-138G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0315 in 825,616 control chromosomes in the GnomAD database, including 1,358 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 0.069 (855 hom., cov: 32)
  • Exomes 𝑓: 0.023 (503 hom.)
• Consequence: SLCO2B1 NM_007256.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.730
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO2B1	NM_007256.5	c.1434-138G>T		intron_variant	Intron 9 of 13	ENST00000289575.10	NP_009187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO2B1	ENST00000289575.10	c.1434-138G>T		intron_variant	Intron 9 of 13	1	NM_007256.5	ENSP00000289575.5

Frequencies

GnomAD3 genomes AF: 0.0688 AC: 10454 AN: 152016 Hom.: 852 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0294

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0334

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0536

GnomAD4 exome AF: 0.0230 AC: 15503 AN: 673482 Hom.: 503 Cov.: 9 AF XY: 0.0224 AC XY: 7677 AN XY: 343226

African (AFR) AF: 0.198 AC: 3155 AN: 15900

American (AMR) AF: 0.0204 AC: 389 AN: 19054

Ashkenazi Jewish (ASJ) AF: 0.0494 AC: 738 AN: 14938

East Asian (EAS) AF: 0.0288 AC: 907 AN: 31462

South Asian (SAS) AF: 0.0150 AC: 746 AN: 49864

European-Finnish (FIN) AF: 0.0301 AC: 1197 AN: 39772

Middle Eastern (MID) AF: 0.0225 AC: 64 AN: 2846

European-Non Finnish (NFE) AF: 0.0154 AC: 7173 AN: 466558

Other (OTH) AF: 0.0343 AC: 1134 AN: 33088

GnomAD4 genome AF: 0.0688 AC: 10469 AN: 152134 Hom.: 855 Cov.: 32 AF XY: 0.0674 AC XY: 5011 AN XY: 74388

African (AFR) AF: 0.193 AC: 8004 AN: 41462

American (AMR) AF: 0.0294 AC: 449 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3470

East Asian (EAS) AF: 0.0321 AC: 166 AN: 5168

South Asian (SAS) AF: 0.0124 AC: 60 AN: 4824

European-Finnish (FIN) AF: 0.0334 AC: 354 AN: 10610

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0165 AC: 1123 AN: 67992

Other (OTH) AF: 0.0530 AC: 112 AN: 2112

Alfa AF: 0.0259 Hom.: 338

Bravo AF: 0.0728

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.83
PhyloP100		0.73
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: rs2306167; hg19: chr11-74907421;