15-91941607-G-T

Position:

• chr15-91941607-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

SLCO3A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.646+25149G>T		intron_variant		ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.646+25149G>T		intron_variant			NP_001138516.1
SLCO3A1	NR_135775.2	n.573+25149G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.646+25149G>T		intron_variant		1	NM_013272.4	ENSP00000320634.6

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

GnomAD3 exomes AF: 0.0550 AC: 7032 AN: 127750 Hom.: 272 AF XY: 0.0532 AC XY: 3721 AN XY: 69958

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 SAS exome AF: 0.0223

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

Gnomad4 AFR exome AF: 0.0664

Gnomad4 AMR exome AF: 0.0334

Gnomad4 ASJ exome AF: 0.0411

Gnomad4 EAS exome AF: 0.00141

Gnomad4 SAS exome AF: 0.0225

Gnomad4 FIN exome AF: 0.118

Gnomad4 NFE exome AF: 0.0894

Gnomad4 OTH exome AF: 0.0699

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

Gnomad4 AFR AF: 0.0687

Gnomad4 AMR AF: 0.0447

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0218

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0897

Gnomad4 OTH AF: 0.0752

Alfa AF: 0.0777 Hom.: 412

Bravo AF: 0.0684

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs8027174; hg19: chr15-92484837;