chr11-75196376-G-A

Variant names:

• chr11-75196376-G-A
• rs2306167
• NM_007256.5:c.1434-138G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_007256.5(SLCO2B1):​c.1434-138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 673610 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 343282

African (AFR) AF: 0.00 AC: 0 AN: 15926

American (AMR) AF: 0.00 AC: 0 AN: 19056

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14946

East Asian (EAS) AF: 0.00 AC: 0 AN: 31462

South Asian (SAS) AF: 0.00 AC: 0 AN: 49864

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39774

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2846

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 466642

Other (OTH) AF: 0.00 AC: 0 AN: 33094

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.81
PhyloP100		0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;