rs207960

Positions:

• chr15-92111489-A-C

Variant summary

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

The NM_013272.4(SLCO3A1):​c.1009+6947A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 151,918 control chromosomes in the GnomAD database, including 43,337 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 0.75 (43337 hom., cov: 30)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1009+6947A>C		intron_variant		ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1009+6947A>C		intron_variant			NP_001138516.1
SLCO3A1	NR_135775.2	n.936+6947A>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+6947A>C		intron_variant		1	NM_013272.4	ENSP00000320634	P1

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114483 AN: 151800 Hom.: 43266 Cov.: 30

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.754 AC: 114614 AN: 151918 Hom.: 43337 Cov.: 30 AF XY: 0.757 AC XY: 56203 AN XY: 74234

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.780

Alfa AF: 0.768 Hom.: 71430

Bravo AF: 0.758

Asia WGS AF: 0.730 AC: 2541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.2
DANN	Benign	0.76

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: rs207960; hg19: chr15-92654719;