rs207974

Variant names:

• chr15-92095422-A-G
• rs207974
• NM_013272.4:c.745+443A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-92095422-A-G
• chr15-92095422-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013272.4(SLCO3A1):​c.745+443A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,198 control chromosomes in the GnomAD database, including 39,996 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 0.72 (39996 hom., cov: 33)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.91
• Publications: 0 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.745+443A>G		intron_variant	Intron 3 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.745+443A>G		intron_variant	Intron 3 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.672+443A>G		intron_variant	Intron 3 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.745+443A>G		intron_variant	Intron 3 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109980 AN: 152080 Hom.: 39942 Cov.: 33

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.723 AC: 110098 AN: 152198 Hom.: 39996 Cov.: 33 AF XY: 0.726 AC XY: 54067 AN XY: 74428

African (AFR) AF: 0.663 AC: 27502 AN: 41502

American (AMR) AF: 0.820 AC: 12535 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2918 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3105 AN: 5174

South Asian (SAS) AF: 0.749 AC: 3611 AN: 4824

European-Finnish (FIN) AF: 0.744 AC: 7887 AN: 10596

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50124 AN: 68018

Other (OTH) AF: 0.749 AC: 1583 AN: 2114

Alfa AF: 0.733 Hom.: 174882

Bravo AF: 0.725

Asia WGS AF: 0.692 AC: 2407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0070
DANN	Benign	0.37
PhyloP100		-4.9
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: rs207974; hg19: chr15-92638652;