rs1517620

Positions:

• chr15-92107033-T-C
• chr15-92107033-T-G

Variant summary

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

The NM_013272.4(SLCO3A1):​c.1009+2491T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,042 control chromosomes in the GnomAD database, including 30,655 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 0.61 (30655 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1009+2491T>C		intron_variant		ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1009+2491T>C		intron_variant			NP_001138516.1
SLCO3A1	NR_135775.2	n.936+2491T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1009+2491T>C		intron_variant		1	NM_013272.4	ENSP00000320634	P1

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93247 AN: 151924 Hom.: 30634 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.614 AC: 93301 AN: 152042 Hom.: 30655 Cov.: 32 AF XY: 0.620 AC XY: 46051 AN XY: 74312

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.672

Alfa AF: 0.696 Hom.: 36283

Bravo AF: 0.606

Asia WGS AF: 0.685 AC: 2382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.085
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs1517620; hg19: chr15-92650263;