rs12726299

Positions:

• chr1-115983051-G-A

Variant summary

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

The NM_018420.3(SLC22A15):​c.87+6337G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,070 control chromosomes in the GnomAD database, including 19,071 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 0.47 (19071 hom., cov: 33)
• Consequence: SLC22A15 NM_018420.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

SLC22A15 (HGNC:20301): (solute carrier family 22 member 15) Organic ion transporters, such as SLC22A15, transport various medically and physiologically important compounds, including pharmaceuticals, toxins, hormones, neurotransmitters, and cellular metabolites. These transporters are also referred to as amphiphilic solute facilitators (ASFs).[supplied by OMIM, Apr 2004]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A15	NM_018420.3	c.87+6337G>A		intron_variant		ENST00000369503.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A15	ENST00000369503.9	c.87+6337G>A		intron_variant		1	NM_018420.3	P1
SLC22A15	ENST00000369502.1	c.87+6337G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71140 AN: 151952 Hom.: 19076 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.468 AC: 71134 AN: 152070 Hom.: 19071 Cov.: 33 AF XY: 0.466 AC XY: 34653 AN XY: 74338

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.486

Alfa AF: 0.573 Hom.: 32523

Bravo AF: 0.444

Asia WGS AF: 0.488 AC: 1696 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.32

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: rs12726299; hg19: chr1-116525672;