12-21334134-C-T

Variant names:

• chr12-21334134-C-T
• rs4148981
• NM_001386879.1:c.60+454G>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.60+454G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,844 control chromosomes in the GnomAD database, including 10,649 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 0.36 (10649 hom., cov: 33)
• Consequence: SLCO1A2 NM_001386879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO1A2	NM_001386879.1	c.60+454G>A		intron_variant	Intron 2 of 14	ENST00000683939.1	NP_001373808.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO1A2	ENST00000683939.1	c.60+454G>A		intron_variant	Intron 2 of 14		NM_001386879.1	ENSP00000508235.1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55249 AN: 151726 Hom.: 10626 Cov.: 33

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.364 AC: 55314 AN: 151844 Hom.: 10649 Cov.: 33 AF XY: 0.362 AC XY: 26888 AN XY: 74196

African (AFR) AF: 0.489 AC: 20266 AN: 41436

American (AMR) AF: 0.252 AC: 3838 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1240 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1789 AN: 5156

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4816

European-Finnish (FIN) AF: 0.344 AC: 3635 AN: 10556

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.320 AC: 21725 AN: 67874

Other (OTH) AF: 0.357 AC: 753 AN: 2112

Alfa AF: 0.340 Hom.: 13378

Bravo AF: 0.363

Asia WGS AF: 0.326 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.038
DANN	Benign	0.14
PhyloP100		-2.3
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: rs4148981; hg19: chr12-21487068;