15-91994615-T-C

Variant names:

• chr15-91994615-T-C
• rs4932598
• NM_013272.4:c.646+78157T>C

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+78157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,248 control chromosomes in the GnomAD database, including 2,915 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 0.18 (2915 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 3 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013272.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	NM_013272.4	MANE Select	c.646+78157T>C		intron	N/A	NP_037404.2
	SLCO3A1	NM_001145044.1		c.646+78157T>C		intron	N/A	NP_001138516.1
	SLCO3A1	NR_135775.2		n.573+78157T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	ENST00000318445.11	TSL:1 MANE Select	c.646+78157T>C		intron	N/A	ENSP00000320634.6
	SLCO3A1	ENST00000424469.2	TSL:1	c.646+78157T>C		intron	N/A	ENSP00000387846.2
	SLCO3A1	ENST00000555769.5	TSL:1	n.541+78157T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27012 AN: 152130 Hom.: 2907 Cov.: 32

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.177 AC: 27021 AN: 152248 Hom.: 2915 Cov.: 32 AF XY: 0.184 AC XY: 13682 AN XY: 74452

African (AFR) AF: 0.0896 AC: 3724 AN: 41558

American (AMR) AF: 0.298 AC: 4550 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3470

East Asian (EAS) AF: 0.330 AC: 1709 AN: 5184

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4820

European-Finnish (FIN) AF: 0.233 AC: 2466 AN: 10604

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11992 AN: 68002

Other (OTH) AF: 0.184 AC: 389 AN: 2116

Alfa AF: 0.188 Hom.: 1181

Bravo AF: 0.180

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.89
DANN	Benign	0.71
PhyloP100		-0.64
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: rs4932598; hg19: chr15-92537845; COSMIC: COSV59238255;