rs4149000

Variant names:

• chr12-21295063-C-T
• rs4149000
• NM_001386879.1:c.1271+534G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001386879.1(SLCO1A2):​c.1271+534G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 151,890 control chromosomes in the GnomAD database, including 1,090 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 0.11 (1089 hom., cov: 32)
  • Exomes 𝑓: 0.15 (1 hom.)
• Consequence: SLCO1A2 NM_001386879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO1A2	NM_001386879.1	c.1271+534G>A		intron_variant	Intron 10 of 14	ENST00000683939.1	NP_001373808.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO1A2	ENST00000683939.1	c.1271+534G>A		intron_variant	Intron 10 of 14		NM_001386879.1	ENSP00000508235.1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16085 AN: 151728 Hom.: 1090 Cov.: 32

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0446

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.119

GnomAD4 exome AF: 0.152 AC: 7 AN: 46 Hom.: 1 Cov.: 0 AF XY: 0.133 AC XY: 4 AN XY: 30

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.184 AC: 7 AN: 38

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.106 AC: 16084 AN: 151844 Hom.: 1089 Cov.: 32 AF XY: 0.108 AC XY: 8034 AN XY: 74182

African (AFR) AF: 0.0286 AC: 1187 AN: 41466

American (AMR) AF: 0.122 AC: 1859 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3462

East Asian (EAS) AF: 0.108 AC: 556 AN: 5150

South Asian (SAS) AF: 0.0445 AC: 214 AN: 4814

European-Finnish (FIN) AF: 0.188 AC: 1974 AN: 10524

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9566 AN: 67880

Other (OTH) AF: 0.117 AC: 248 AN: 2114

Alfa AF: 0.132 Hom.: 2339

Bravo AF: 0.0978

Asia WGS AF: 0.0800 AC: 275 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.59
PhyloP100		-1.4
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: rs4149000; hg19: chr12-21447997;