rs8027174

Variant names:

• chr15-91941607-G-T
• rs8027174
• NM_013272.4:c.646+25149G>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+25149G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0689 in 455,534 control chromosomes in the GnomAD database, including 1,325 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 0.075 (490 hom., cov: 32)
  • Exomes 𝑓: 0.066 (835 hom.)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0878 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.646+25149G>T		intron	N/A	NP_037404.2	Q9UIG8-1
	SLCO3A1	NM_001145044.1		c.646+25149G>T		intron	N/A	NP_001138516.1	Q9UIG8-2
	SLCO3A1	NR_135775.2		n.573+25149G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	ENST00000318445.11	TSL:1 MANE Select	c.646+25149G>T		intron	N/A	ENSP00000320634.6	Q9UIG8-1
	SLCO3A1	ENST00000424469.2	TSL:1	c.646+25149G>T		intron	N/A	ENSP00000387846.2	Q9UIG8-2
	SLCO3A1	ENST00000555769.5	TSL:1	n.541+25149G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0748 AC: 11373 AN: 152076 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0447

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0897

Gnomad OTH AF: 0.0712

GnomAD2 exomes AF: 0.0550 AC: 7032 AN: 127750 AF XY: 0.0532

Gnomad AFR exome AF: 0.0687

Gnomad AMR exome AF: 0.0327

Gnomad ASJ exome AF: 0.0422

Gnomad EAS exome AF: 0.000767

Gnomad FIN exome AF: 0.116

Gnomad NFE exome AF: 0.0872

Gnomad OTH exome AF: 0.0576

GnomAD4 exome AF: 0.0658 AC: 19970 AN: 303340 Hom.: 835 Cov.: 0 AF XY: 0.0610 AC XY: 10537 AN XY: 172780

African (AFR) AF: 0.0664 AC: 570 AN: 8590

American (AMR) AF: 0.0334 AC: 910 AN: 27216

Ashkenazi Jewish (ASJ) AF: 0.0411 AC: 443 AN: 10774

East Asian (EAS) AF: 0.00141 AC: 13 AN: 9198

South Asian (SAS) AF: 0.0225 AC: 1340 AN: 59650

European-Finnish (FIN) AF: 0.118 AC: 1462 AN: 12356

Middle Eastern (MID) AF: 0.0227 AC: 63 AN: 2774

European-Non Finnish (NFE) AF: 0.0894 AC: 14178 AN: 158598

Other (OTH) AF: 0.0699 AC: 991 AN: 14184

GnomAD4 genome AF: 0.0749 AC: 11400 AN: 152194 Hom.: 490 Cov.: 32 AF XY: 0.0727 AC XY: 5412 AN XY: 74402

African (AFR) AF: 0.0687 AC: 2853 AN: 41518

American (AMR) AF: 0.0447 AC: 684 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5180

South Asian (SAS) AF: 0.0218 AC: 105 AN: 4818

European-Finnish (FIN) AF: 0.121 AC: 1279 AN: 10572

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0897 AC: 6100 AN: 68006

Other (OTH) AF: 0.0752 AC: 159 AN: 2114

Alfa AF: 0.0797 Hom.: 1255

Bravo AF: 0.0684

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.50
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs8027174; hg19: chr15-92484837;