chr15-92165073-C-T

Position:

• chr15-92165073-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.*1938C>T		3_prime_UTR_variant	10/10	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1996+2075C>T		intron_variant			NP_001138516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.*1938C>T		3_prime_UTR_variant	10/10	1	NM_013272.4	ENSP00000320634.6

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

Gnomad4 AFR exome AF: 0.651

Gnomad4 AMR exome AF: 0.651

Gnomad4 ASJ exome AF: 0.691

Gnomad4 EAS exome AF: 0.233

Gnomad4 SAS exome AF: 0.465

Gnomad4 FIN exome AF: 0.598

Gnomad4 NFE exome AF: 0.635

Gnomad4 OTH exome AF: 0.603

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

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.645

Alfa AF: 0.626 Hom.: 27014

Bravo AF: 0.631

Asia WGS AF: 0.388 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.1
DANN	Benign	0.54

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

Publications

LitVar

Other links and lift over

dbSNP: rs7496880; hg19: chr15-92708303;