chr12-21339003-A-T

Variant names:

• chr12-21339003-A-T
• rs2857468
• ENST00000307378.10:c.-62-4294T>A

Variant summary

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

The NM_134431.5(SLCO1A2):​c.-62-4294T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 151,922 control chromosomes in the GnomAD database, including 53,012 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 0.83 (53012 hom., cov: 32)
• Consequence: SLCO1A2 NM_134431.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_134431.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO1A2	NM_001386878.1		c.-62-4294T>A		intron	N/A	NP_001373807.1	P46721-1
	SLCO1A2	NM_001386881.1		c.-57-4299T>A		intron	N/A	NP_001373810.1	P46721-1
	SLCO1A2	NM_001386882.2		c.-62-4294T>A		intron	N/A	NP_001373811.1	P46721-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO1A2	ENST00000307378.10	TSL:1	c.-62-4294T>A		intron	N/A	ENSP00000305974.6	P46721-1
	SLCO1A2	ENST00000938257.1		c.-57-4299T>A		intron	N/A	ENSP00000608316.1
	SLCO1A2	ENST00000938258.1		c.-57-4299T>A		intron	N/A	ENSP00000608317.1

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126100 AN: 151804 Hom.: 52986 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.831 AC: 126175 AN: 151922 Hom.: 53012 Cov.: 32 AF XY: 0.836 AC XY: 62069 AN XY: 74254

African (AFR) AF: 0.696 AC: 28854 AN: 41454

American (AMR) AF: 0.890 AC: 13548 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2849 AN: 3468

East Asian (EAS) AF: 0.997 AC: 5132 AN: 5146

South Asian (SAS) AF: 0.918 AC: 4427 AN: 4822

European-Finnish (FIN) AF: 0.895 AC: 9485 AN: 10600

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59269 AN: 67902

Other (OTH) AF: 0.819 AC: 1729 AN: 2110

Alfa AF: 0.851 Hom.: 6921

Bravo AF: 0.823

Asia WGS AF: 0.940 AC: 3262 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.69
PhyloP100		0.49
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: rs2857468; hg19: chr12-21491937;