15-92114143-T-C

Variant names:

• chr15-92114143-T-C
• rs207954
• NM_013272.4:c.1010-6322T>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.1010-6322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 151,932 control chromosomes in the GnomAD database, including 36,528 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 0.69 (36528 hom., cov: 31)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1010-6322T>C		intron_variant	Intron 4 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1010-6322T>C		intron_variant	Intron 4 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.937-6322T>C		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1010-6322T>C		intron_variant	Intron 4 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104531 AN: 151814 Hom.: 36500 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.688 AC: 104600 AN: 151932 Hom.: 36528 Cov.: 31 AF XY: 0.691 AC XY: 51322 AN XY: 74268

African (AFR) AF: 0.557 AC: 23058 AN: 41430

American (AMR) AF: 0.787 AC: 12004 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2878 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3703 AN: 5138

South Asian (SAS) AF: 0.743 AC: 3574 AN: 4812

European-Finnish (FIN) AF: 0.711 AC: 7517 AN: 10566

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49403 AN: 67942

Other (OTH) AF: 0.736 AC: 1551 AN: 2108

Alfa AF: 0.718 Hom.: 179368

Bravo AF: 0.689

Asia WGS AF: 0.711 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.39
PhyloP100		-0.040
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: rs207954; hg19: chr15-92657373;