15-92165073-C-T

Variant names:

• chr15-92165073-C-T
• rs7496880
• NM_013272.4:c.*1938C>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.*1938C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 984,936 control chromosomes in the GnomAD database, including 195,314 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 (29343 hom., cov: 32)
  • Exomes 𝑓: 0.63 (165971 hom.)
• Consequence: SLCO3A1 NM_013272.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.644 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.*1938C>T		3_prime_UTR	Exon 10 of 10	NP_037404.2
	SLCO3A1	NM_001145044.1		c.1996+2075C>T		intron	N/A	NP_001138516.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	ENST00000318445.11	TSL:1 MANE Select	c.*1938C>T		3_prime_UTR	Exon 10 of 10	ENSP00000320634.6
	SLCO3A1	ENST00000424469.2	TSL:1	c.1996+2075C>T		intron	N/A	ENSP00000387846.2
	ENSG00000260661	ENST00000561674.1	TSL:1	n.186-7832G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93586 AN: 151944 Hom.: 29324 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.651

GnomAD4 exome AF: 0.630 AC: 524746 AN: 832874 Hom.: 165971 Cov.: 35 AF XY: 0.631 AC XY: 242557 AN XY: 384598

African (AFR) AF: 0.651 AC: 10270 AN: 15784

American (AMR) AF: 0.651 AC: 641 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 3561 AN: 5152

East Asian (EAS) AF: 0.233 AC: 844 AN: 3630

South Asian (SAS) AF: 0.465 AC: 7655 AN: 16454

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

Middle Eastern (MID) AF: 0.732 AC: 1186 AN: 1620

European-Non Finnish (NFE) AF: 0.635 AC: 483967 AN: 761682

Other (OTH) AF: 0.603 AC: 16457 AN: 27292

GnomAD4 genome AF: 0.616 AC: 93647 AN: 152062 Hom.: 29343 Cov.: 32 AF XY: 0.609 AC XY: 45239 AN XY: 74322

African (AFR) AF: 0.638 AC: 26474 AN: 41484

American (AMR) AF: 0.654 AC: 10000 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2396 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1251 AN: 5168

South Asian (SAS) AF: 0.457 AC: 2200 AN: 4812

European-Finnish (FIN) AF: 0.584 AC: 6162 AN: 10552

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

European-Non Finnish (NFE) AF: 0.634 AC: 43126 AN: 67976

Other (OTH) AF: 0.645 AC: 1362 AN: 2112

Alfa AF: 0.630 Hom.: 41780

Bravo AF: 0.631

Asia WGS AF: 0.388 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.1
DANN	Benign	0.54
PhyloP100		1.6
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: rs7496880; hg19: chr15-92708303;