chr15-92110374-C-G

Variant names:

• chr15-92110374-C-G
• rs207961
• NM_013272.4:c.1009+5832C>G

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+5832C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,084 control chromosomes in the GnomAD database, including 7,348 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 0.31 (7348 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789
• Publications: 2 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=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013272.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	NM_013272.4	MANE Select	c.1009+5832C>G		intron	N/A	NP_037404.2
	SLCO3A1	NM_001145044.1		c.1009+5832C>G		intron	N/A	NP_001138516.1
	SLCO3A1	NR_135775.2		n.936+5832C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	ENST00000318445.11	TSL:1 MANE Select	c.1009+5832C>G		intron	N/A	ENSP00000320634.6
	SLCO3A1	ENST00000424469.2	TSL:1	c.1009+5832C>G		intron	N/A	ENSP00000387846.2
	SLCO3A1	ENST00000555769.5	TSL:1	n.904+5832C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46944 AN: 151964 Hom.: 7341 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.309 AC: 46970 AN: 152084 Hom.: 7348 Cov.: 32 AF XY: 0.311 AC XY: 23106 AN XY: 74348

African (AFR) AF: 0.267 AC: 11083 AN: 41476

American (AMR) AF: 0.339 AC: 5185 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3470

East Asian (EAS) AF: 0.185 AC: 955 AN: 5166

South Asian (SAS) AF: 0.353 AC: 1702 AN: 4820

European-Finnish (FIN) AF: 0.373 AC: 3950 AN: 10580

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21828 AN: 67968

Other (OTH) AF: 0.333 AC: 701 AN: 2106

Alfa AF: 0.318 Hom.: 997

Bravo AF: 0.308

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.9
DANN	Benign	0.78
PhyloP100		0.79
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: rs207961; hg19: chr15-92653604;