chr12-21380234-T-C

Position:

• chr12-21380234-T-C

Variant summary

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

The NM_134431.5(SLCO1A2):​c.-189-5709A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,172 control chromosomes in the GnomAD database, including 3,468 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 (3468 hom., cov: 32)
• Consequence: SLCO1A2 NM_134431.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

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]

SLCO1A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO1A2	NM_001386878.1	c.-63+23185A>G		intron_variant			NP_001373807.1
SLCO1A2	NM_001386881.1	c.-58+37648A>G		intron_variant			NP_001373810.1
SLCO1A2	NM_134431.5	c.-189-5709A>G		intron_variant			NP_602307.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO1A2	ENST00000307378.10	c.-189-5709A>G		intron_variant		1		ENSP00000305974.6
SLCO1A2	ENST00000453443.5	c.-63+23185A>G		intron_variant		3		ENSP00000409314.1
SLCO1A2	ENST00000450590.5	c.-58+23185A>G		intron_variant		4		ENSP00000407462.1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29407 AN: 152054 Hom.: 3472 Cov.: 32

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.193 AC: 29387 AN: 152172 Hom.: 3468 Cov.: 32 AF XY: 0.192 AC XY: 14319 AN XY: 74392

Gnomad4 AFR AF: 0.0545

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.211

Alfa AF: 0.228 Hom.: 790

Bravo AF: 0.195

Asia WGS AF: 0.221 AC: 760 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.79

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: rs2417977; hg19: chr12-21533168;