chr15-92089345-T-A

Variant names:

• chr15-92089345-T-A
• rs1983350
• NM_013272.4:c.647-5536T>A

Variant summary

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

The NM_013272.4(SLCO3A1):​c.647-5536T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,076 control chromosomes in the GnomAD database, including 39,367 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 (39367 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 1 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 = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.647-5536T>A		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.647-5536T>A		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.574-5536T>A		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.647-5536T>A		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109124 AN: 151956 Hom.: 39292 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.718 AC: 109260 AN: 152076 Hom.: 39367 Cov.: 32 AF XY: 0.720 AC XY: 53513 AN XY: 74344

African (AFR) AF: 0.722 AC: 29946 AN: 41476

American (AMR) AF: 0.802 AC: 12263 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2845 AN: 3470

East Asian (EAS) AF: 0.576 AC: 2967 AN: 5154

South Asian (SAS) AF: 0.680 AC: 3283 AN: 4826

European-Finnish (FIN) AF: 0.734 AC: 7741 AN: 10550

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47948 AN: 67986

Other (OTH) AF: 0.739 AC: 1560 AN: 2112

Alfa AF: 0.720 Hom.: 4904

Bravo AF: 0.723

Asia WGS AF: 0.648 AC: 2254 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	0.22
DANN	Benign	0.68
PhyloP100		-1.0
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: rs1983350; hg19: chr15-92632575;