rs16923647

Variant names:

• chr12-21298461-C-T
• rs16923647
• NM_001386879.1:c.911-893G>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.911-893G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,164 control chromosomes in the GnomAD database, including 1,020 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 0.10 (1020 hom., cov: 32)
• Consequence: SLCO1A2 NM_001386879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794
• Publications: 12 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO1A2	NM_001386879.1	c.911-893G>A		intron_variant	Intron 8 of 14	ENST00000683939.1	NP_001373808.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO1A2	ENST00000683939.1	c.911-893G>A		intron_variant	Intron 8 of 14		NM_001386879.1	ENSP00000508235.1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15578 AN: 152046 Hom.: 1021 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.102 AC: 15577 AN: 152164 Hom.: 1020 Cov.: 32 AF XY: 0.105 AC XY: 7804 AN XY: 74380

African (AFR) AF: 0.0276 AC: 1145 AN: 41546

American (AMR) AF: 0.118 AC: 1803 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0988 AC: 343 AN: 3470

East Asian (EAS) AF: 0.108 AC: 557 AN: 5154

South Asian (SAS) AF: 0.0433 AC: 209 AN: 4828

European-Finnish (FIN) AF: 0.185 AC: 1963 AN: 10584

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9213 AN: 67994

Other (OTH) AF: 0.113 AC: 239 AN: 2112

Alfa AF: 0.123 Hom.: 3784

Bravo AF: 0.0939

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.2
DANN	Benign	0.37
PhyloP100		-0.79
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs16923647; hg19: chr12-21451395;