chr15-92090903-A-G

Position:

• chr15-92090903-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013272.4(SLCO3A1):​c.647-3978A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,012 control chromosomes in the GnomAD database, including 23,110 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 0.53 (23110 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.647-3978A>G		intron_variant		ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.647-3978A>G		intron_variant			NP_001138516.1
SLCO3A1	NR_135775.2	n.574-3978A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.647-3978A>G		intron_variant		1	NM_013272.4	ENSP00000320634	P1

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79806 AN: 151894 Hom.: 23104 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.525 AC: 79837 AN: 152012 Hom.: 23110 Cov.: 32 AF XY: 0.525 AC XY: 38992 AN XY: 74308

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.579

Alfa AF: 0.632 Hom.: 47962

Bravo AF: 0.506

Asia WGS AF: 0.371 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.022
DANN	Benign	0.33

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

Publications

LitVar

Other links and lift over

dbSNP: rs871167; hg19: chr15-92634133;