rs207960

Variant names:

• chr15-92111489-A-C
• rs207960
• NM_013272.4:c.1009+6947A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1009+6947A>C		intron_variant	Intron 4 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1009+6947A>C		intron_variant	Intron 4 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.936+6947A>C		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1009+6947A>C		intron_variant	Intron 4 of 9	1	NM_013272.4	ENSP00000320634.6

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

African (AFR) AF: 0.704 AC: 29166 AN: 41420

American (AMR) AF: 0.837 AC: 12775 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2957 AN: 3468

East Asian (EAS) AF: 0.719 AC: 3689 AN: 5132

South Asian (SAS) AF: 0.749 AC: 3587 AN: 4788

European-Finnish (FIN) AF: 0.759 AC: 8017 AN: 10562

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51945 AN: 67972

Other (OTH) AF: 0.780 AC: 1642 AN: 2106

Alfa AF: 0.762 Hom.: 167004

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
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs207960; hg19: chr15-92654719;