15-92061300-T-C

Variant names:

• chr15-92061300-T-C
• rs12899055
• NM_013272.4:c.647-33581T>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.647-33581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,998 control chromosomes in the GnomAD database, including 27,953 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.60 (27953 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.558
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.736 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	NM_013272.4	MANE Select	c.647-33581T>C		intron	N/A	NP_037404.2	Q9UIG8-1
	SLCO3A1	NM_001145044.1		c.647-33581T>C		intron	N/A	NP_001138516.1	Q9UIG8-2
	SLCO3A1	NR_135775.2		n.574-33581T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	ENST00000318445.11	TSL:1 MANE Select	c.647-33581T>C		intron	N/A	ENSP00000320634.6	Q9UIG8-1
	SLCO3A1	ENST00000424469.2	TSL:1	c.647-33581T>C		intron	N/A	ENSP00000387846.2	Q9UIG8-2
	SLCO3A1	ENST00000555769.5	TSL:1	n.542-33581T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90667 AN: 151882 Hom.: 27930 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.597 AC: 90734 AN: 151998 Hom.: 27953 Cov.: 32 AF XY: 0.598 AC XY: 44432 AN XY: 74282

African (AFR) AF: 0.432 AC: 17914 AN: 41434

American (AMR) AF: 0.748 AC: 11419 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2411 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3172 AN: 5158

South Asian (SAS) AF: 0.634 AC: 3053 AN: 4814

European-Finnish (FIN) AF: 0.613 AC: 6470 AN: 10556

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44272 AN: 67974

Other (OTH) AF: 0.645 AC: 1360 AN: 2110

Alfa AF: 0.635 Hom.: 84143

Bravo AF: 0.603

Asia WGS AF: 0.636 AC: 2211 AN: 3478

ClinVar

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Vascular endothelial growth factor (VEGF) inhibitor response (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.54
PhyloP100		-0.56
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: rs12899055; hg19: chr15-92604530;