rs10743413

chr12-21354140-T-Cchr12-21354140-T-G

Variant summary

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

The ENST00000307378.10(SLCO1A2):c.-62-19431A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,068 control chromosomes in the GnomAD database, including 3,698 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 0.20 (3698 hom., cov: 32)
• Consequence: SLCO1A2 ENST00000307378.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

Genes affected

SLCO1A2 (HGNC:10956): (solute carrier organic anion transporter family member 1A2) This gene encodes a sodium-independent transporter which mediates cellular uptake of organic ions in the liver. Its substrates include bile acids, bromosulphophthalein, and some steroidal compounds. The protein is a member of the SLC21A family of solute carriers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO1A2	NM_001386878.1	c.-62-19431A>G		intron_variant
SLCO1A2	NM_001386881.1	c.-57-19436A>G		intron_variant
SLCO1A2	NM_001386882.2	c.-63+6523A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO1A2	ENST00000307378.10	c.-62-19431A>G		intron_variant		1		P1
SLCO1A2	ENST00000413682.5	c.-311-19436A>G		intron_variant		4
SLCO1A2	ENST00000416627.1	c.-62-19431A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30776 AN: 151948 Hom.: 3690 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.203 AC: 30819 AN: 152068 Hom.: 3698 Cov.: 32 AF XY: 0.207 AC XY: 15387 AN XY: 74350

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.186

Alfa AF: 0.156 Hom.: 1983

Bravo AF: 0.198

Asia WGS AF: 0.325 AC: 1131 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	1.9
Dann	Benign	0.77

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: rs10743413; hg19: chr12-21507074;