rs4115170

Variant names:

• chr12-21322029-T-C
• rs4115170
• NM_001386879.1:c.61-3106A>G

Variant summary

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

The NM_001386879.1(SLCO1A2):​c.61-3106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,062 control chromosomes in the GnomAD database, including 7,738 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 0.32 (7738 hom., cov: 32)
• Consequence: SLCO1A2 NM_001386879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO1A2	NM_001386879.1	c.61-3106A>G		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.61-3106A>G		intron_variant	Intron 2 of 14		NM_001386879.1	ENSP00000508235.1

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48000 AN: 151944 Hom.: 7725 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.316 AC: 48044 AN: 152062 Hom.: 7738 Cov.: 32 AF XY: 0.317 AC XY: 23561 AN XY: 74324

African (AFR) AF: 0.325 AC: 13453 AN: 41452

American (AMR) AF: 0.228 AC: 3487 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1231 AN: 3470

East Asian (EAS) AF: 0.351 AC: 1813 AN: 5172

South Asian (SAS) AF: 0.307 AC: 1484 AN: 4828

European-Finnish (FIN) AF: 0.344 AC: 3637 AN: 10576

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21662 AN: 67974

Other (OTH) AF: 0.318 AC: 672 AN: 2112

Alfa AF: 0.318 Hom.: 12374

Bravo AF: 0.308

Asia WGS AF: 0.320 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0050
DANN	Benign	0.67
PhyloP100		-2.6
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: rs4115170; hg19: chr12-21474963;