rs11045919

Positions:

• chr12-21269319-T-G

Variant summary

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

The NM_001386879.1(SLCO1A2):​c.*229A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 352,198 control chromosomes in the GnomAD database, including 5,925 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 0.19 (3650 hom., cov: 32)
  • Exomes 𝑓: 0.13 (2275 hom.)
• Consequence: SLCO1A2 NM_001386879.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO1A2	NM_001386879.1	c.*229A>C		3_prime_UTR_variant	15/15	ENST00000683939.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO1A2	ENST00000683939.1	c.*229A>C		3_prime_UTR_variant	15/15		NM_001386879.1	P1
SLCO1A2	ENST00000307378.10	c.*229A>C		3_prime_UTR_variant	16/16	1		P1
SLCO1A2	ENST00000544020.5			downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29285 AN: 151700 Hom.: 3634 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0581

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.170

GnomAD4 exome AF: 0.134 AC: 26929 AN: 200380 Hom.: 2275 Cov.: 2 AF XY: 0.132 AC XY: 13827 AN XY: 104416

Gnomad4 AFR exome AF: 0.368

Gnomad4 AMR exome AF: 0.0957

Gnomad4 ASJ exome AF: 0.155

Gnomad4 EAS exome AF: 0.0000626

Gnomad4 SAS exome AF: 0.0524

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.145

Gnomad4 OTH exome AF: 0.148

GnomAD4 genome AF: 0.193 AC: 29351 AN: 151818 Hom.: 3650 Cov.: 32 AF XY: 0.188 AC XY: 13968 AN XY: 74218

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0580

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.169

Alfa AF: 0.150 Hom.: 3518

Bravo AF: 0.200

Asia WGS AF: 0.0580 AC: 206 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.2
DANN	Benign	0.82

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: rs11045919; hg19: chr12-21422253;