15-92157973-C-T

Position:

• chr15-92157973-C-T

Variant summary

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

The NM_013272.4(SLCO3A1):​c.1754-4783C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,092 control chromosomes in the GnomAD database, including 44,656 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 0.76 (44656 hom., cov: 31)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

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]

ENSG00000260661 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1754-4783C>T		intron_variant		ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1754-4783C>T		intron_variant			NP_001138516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1754-4783C>T		intron_variant		1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115551 AN: 151974 Hom.: 44600 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.761 AC: 115670 AN: 152092 Hom.: 44656 Cov.: 31 AF XY: 0.753 AC XY: 55998 AN XY: 74332

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.762

Alfa AF: 0.728 Hom.: 51348

Bravo AF: 0.781

Asia WGS AF: 0.630 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.43

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: rs6496898; hg19: chr15-92701203;