chr15-91992321-C-T

Variant names:

• chr15-91992321-C-T
• rs12439738
• NM_013272.4:c.646+75863C>T

Variant summary

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

The NM_013272.4(SLCO3A1):​c.646+75863C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,078 control chromosomes in the GnomAD database, including 6,883 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 0.29 (6883 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590
• Publications: 4 publications found

Genes affected

SLCO3A1 (HGNC:10952): (solute carrier organic anion transporter family member 3A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Involved in positive regulation of NF-kappaB transcription factor activity; positive regulation of protein phosphorylation; and prostaglandin transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000294452 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.646+75863C>T		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.646+75863C>T		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.573+75863C>T		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.646+75863C>T		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44217 AN: 151962 Hom.: 6861 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.291 AC: 44280 AN: 152078 Hom.: 6883 Cov.: 32 AF XY: 0.295 AC XY: 21949 AN XY: 74366

African (AFR) AF: 0.366 AC: 15198 AN: 41468

American (AMR) AF: 0.353 AC: 5404 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1744 AN: 5166

South Asian (SAS) AF: 0.275 AC: 1325 AN: 4818

European-Finnish (FIN) AF: 0.327 AC: 3466 AN: 10590

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15296 AN: 67970

Other (OTH) AF: 0.279 AC: 588 AN: 2104

Alfa AF: 0.278 Hom.: 901

Bravo AF: 0.299

Asia WGS AF: 0.336 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.60
PhyloP100		0.59
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: rs12439738; hg19: chr15-92535551;