rs3924426

Positions:

• chr15-91902643-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000318445.11(SLCO3A1):​c.181-13350T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 152,100 control chromosomes in the GnomAD database, including 1,340 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 0.087 (1340 hom., cov: 31)
• Consequence: SLCO3A1 ENST00000318445.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.181-13350T>C		intron_variant		ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.181-13350T>C		intron_variant			NP_001138516.1
SLCO3A1	NR_135775.2	n.108-13350T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.181-13350T>C		intron_variant		1	NM_013272.4	ENSP00000320634	P1

Frequencies

GnomAD3 genomes AF: 0.0869 AC: 13210 AN: 151982 Hom.: 1324 Cov.: 31

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0942

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.0577

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00845

Gnomad OTH AF: 0.0655

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0872 AC: 13265 AN: 152100 Hom.: 1340 Cov.: 31 AF XY: 0.0890 AC XY: 6618 AN XY: 74388

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.0952

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.0576

Gnomad4 SAS AF: 0.0724

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.00845

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0236 Hom.: 370

Bravo AF: 0.0967

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.70

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: rs3924426; hg19: chr15-92445873;