12-21351134-T-C

Position:

• chr12-21351134-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.-62-16425A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,932 control chromosomes in the GnomAD database, including 29,151 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 0.61 (29151 hom., cov: 31)
• Consequence: SLCO1A2 NM_134431.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO1A2	NM_001386878.1	c.-62-16425A>G		intron_variant			NP_001373807.1
SLCO1A2	NM_001386881.1	c.-57-16430A>G		intron_variant			NP_001373810.1
SLCO1A2	NM_001386882.2	c.-63+9529A>G		intron_variant			NP_001373811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO1A2	ENST00000307378.10	c.-62-16425A>G		intron_variant		1		ENSP00000305974.6
SLCO1A2	ENST00000453443.5	c.-62-16425A>G		intron_variant		3		ENSP00000409314.1
SLCO1A2	ENST00000450590.5	c.-57-16430A>G		intron_variant		4		ENSP00000407462.1

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92452 AN: 151814 Hom.: 29133 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.609 AC: 92498 AN: 151932 Hom.: 29151 Cov.: 31 AF XY: 0.610 AC XY: 45309 AN XY: 74266

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.615

Alfa AF: 0.677 Hom.: 45989

Bravo AF: 0.613

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.72

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: rs4762699; hg19: chr12-21504068;