rs11045919

Variant names:

• chr12-21269319-T-G
• rs11045919
• NM_001386879.1:c.*229A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLCO1A2	NM_001386879.1	c.*229A>C		3_prime_UTR_variant	Exon 15 of 15	ENST00000683939.1	NP_001373808.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO1A2	ENST00000683939.1	c.*229A>C		3_prime_UTR_variant	Exon 15 of 15		NM_001386879.1	ENSP00000508235.1

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

African (AFR) AF: 0.368 AC: 2153 AN: 5844

American (AMR) AF: 0.0957 AC: 709 AN: 7410

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 1079 AN: 6940

East Asian (EAS) AF: 0.0000626 AC: 1 AN: 15980

South Asian (SAS) AF: 0.0524 AC: 505 AN: 9632

European-Finnish (FIN) AF: 0.143 AC: 1755 AN: 12252

Middle Eastern (MID) AF: 0.156 AC: 151 AN: 970

European-Non Finnish (NFE) AF: 0.145 AC: 18680 AN: 128554

Other (OTH) AF: 0.148 AC: 1896 AN: 12798

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

African (AFR) AF: 0.357 AC: 14787 AN: 41406

American (AMR) AF: 0.116 AC: 1771 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3466

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5178

South Asian (SAS) AF: 0.0580 AC: 279 AN: 4812

European-Finnish (FIN) AF: 0.133 AC: 1409 AN: 10576

Middle Eastern (MID) AF: 0.155 AC: 45 AN: 290

European-Non Finnish (NFE) AF: 0.148 AC: 10015 AN: 67832

Other (OTH) AF: 0.169 AC: 356 AN: 2110

Alfa AF: 0.162 Hom.: 6430

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
PhyloP100		1.5
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: rs11045919; hg19: chr12-21422253;