15-91994615-T-C

Position:

• chr15-91994615-T-C

Variant summary

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

The NM_013272.4(SLCO3A1):​c.646+78157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,248 control chromosomes in the GnomAD database, including 2,915 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 0.18 (2915 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO3A1	NM_013272.4	c.646+78157T>C		intron_variant		ENST00000318445.11
SLCO3A1	NM_001145044.1	c.646+78157T>C		intron_variant
SLCO3A1	NR_135775.2	n.573+78157T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.646+78157T>C		intron_variant		1	NM_013272.4	P1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27012 AN: 152130 Hom.: 2907 Cov.: 32

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.177 AC: 27021 AN: 152248 Hom.: 2915 Cov.: 32 AF XY: 0.184 AC XY: 13682 AN XY: 74452

Gnomad4 AFR AF: 0.0896

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.184

Alfa AF: 0.190 Hom.: 622

Bravo AF: 0.180

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.89
DANN	Benign	0.71

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: rs4932598; hg19: chr15-92537845; COSMIC: COSV59238255;