rs16974268

Variant names:

• chr15-92115622-C-T
• rs16974268
• NM_013272.4:c.1010-4843C>T

Variant summary

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

The NM_013272.4(SLCO3A1):​c.1010-4843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 151,798 control chromosomes in the GnomAD database, including 44,553 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 0.75 (44553 hom., cov: 28)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1010-4843C>T		intron_variant	Intron 4 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1010-4843C>T		intron_variant	Intron 4 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.937-4843C>T		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1010-4843C>T		intron_variant	Intron 4 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.751 AC: 113985 AN: 151680 Hom.: 44532 Cov.: 28

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.751 AC: 114046 AN: 151798 Hom.: 44553 Cov.: 28 AF XY: 0.757 AC XY: 56188 AN XY: 74182

African (AFR) AF: 0.510 AC: 21082 AN: 41328

American (AMR) AF: 0.859 AC: 13105 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3070 AN: 3468

East Asian (EAS) AF: 0.948 AC: 4903 AN: 5170

South Asian (SAS) AF: 0.902 AC: 4331 AN: 4804

European-Finnish (FIN) AF: 0.807 AC: 8505 AN: 10536

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56374 AN: 67940

Other (OTH) AF: 0.798 AC: 1675 AN: 2100

Alfa AF: 0.806 Hom.: 192821

Bravo AF: 0.743

Asia WGS AF: 0.884 AC: 3076 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	1.6
DANN	Benign	0.42
PhyloP100		-0.18
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: rs16974268; hg19: chr15-92658852;