NM_013272.4:c.*1544T>C

Variant names:

• chr15-92164679-T-C
• rs9302356
• NM_013272.4:c.*1544T>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.*1544T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 984,790 control chromosomes in the GnomAD database, including 197,796 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 0.62 (29628 hom., cov: 32)
  • Exomes 𝑓: 0.63 (168168 hom.)
• Consequence: SLCO3A1 NM_013272.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• 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]

ENSG00000260661 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.645 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.*1544T>C		3_prime_UTR	Exon 10 of 10	NP_037404.2	Q9UIG8-1
	SLCO3A1	NM_001145044.1		c.1996+1681T>C		intron	N/A	NP_001138516.1	Q9UIG8-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	ENST00000318445.11	TSL:1 MANE Select	c.*1544T>C		3_prime_UTR	Exon 10 of 10	ENSP00000320634.6	Q9UIG8-1
	SLCO3A1	ENST00000424469.2	TSL:1	c.1996+1681T>C		intron	N/A	ENSP00000387846.2	Q9UIG8-2
	ENSG00000260661	ENST00000561674.1	TSL:1	n.186-7438A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93978 AN: 151830 Hom.: 29609 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.654

GnomAD4 exome AF: 0.634 AC: 528211 AN: 832842 Hom.: 168168 Cov.: 35 AF XY: 0.635 AC XY: 244175 AN XY: 384604

African (AFR) AF: 0.648 AC: 10223 AN: 15782

American (AMR) AF: 0.654 AC: 644 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 3563 AN: 5150

East Asian (EAS) AF: 0.232 AC: 841 AN: 3630

South Asian (SAS) AF: 0.483 AC: 7945 AN: 16448

European-Finnish (FIN) AF: 0.598 AC: 165 AN: 276

Middle Eastern (MID) AF: 0.737 AC: 1196 AN: 1622

European-Non Finnish (NFE) AF: 0.639 AC: 487059 AN: 761660

Other (OTH) AF: 0.607 AC: 16575 AN: 27290

GnomAD4 genome AF: 0.619 AC: 94036 AN: 151948 Hom.: 29628 Cov.: 32 AF XY: 0.612 AC XY: 45434 AN XY: 74272

African (AFR) AF: 0.641 AC: 26549 AN: 41414

American (AMR) AF: 0.655 AC: 10006 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2396 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1236 AN: 5152

South Asian (SAS) AF: 0.475 AC: 2293 AN: 4826

European-Finnish (FIN) AF: 0.583 AC: 6139 AN: 10530

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43356 AN: 67982

Other (OTH) AF: 0.648 AC: 1361 AN: 2100

Alfa AF: 0.630 Hom.: 36587

Bravo AF: 0.633

Asia WGS AF: 0.397 AC: 1387 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	0.36
DANN	Benign	0.33
PhyloP100		-0.33
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: rs9302356; hg19: chr15-92707909;