chr15-92108943-T-C

Variant names:

• chr15-92108943-T-C
• rs207964
• NM_013272.4:c.1009+4401T>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.1009+4401T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,034 control chromosomes in the GnomAD database, including 61,463 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 0.90 (61463 hom., cov: 30)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.1009+4401T>C		intron_variant	Intron 4 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.1009+4401T>C		intron_variant	Intron 4 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.936+4401T>C		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.1009+4401T>C		intron_variant	Intron 4 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136296 AN: 151916 Hom.: 61395 Cov.: 30

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.897 AC: 136424 AN: 152034 Hom.: 61463 Cov.: 30 AF XY: 0.900 AC XY: 66828 AN XY: 74278

African (AFR) AF: 0.973 AC: 40366 AN: 41500

American (AMR) AF: 0.917 AC: 14003 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3110 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4925 AN: 5124

South Asian (SAS) AF: 0.909 AC: 4368 AN: 4806

European-Finnish (FIN) AF: 0.874 AC: 9228 AN: 10556

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57473 AN: 67988

Other (OTH) AF: 0.909 AC: 1919 AN: 2112

Alfa AF: 0.864 Hom.: 78414

Bravo AF: 0.904

Asia WGS AF: 0.934 AC: 3250 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	3.1
DANN	Benign	0.81
PhyloP100		-0.22
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: rs207964; hg19: chr15-92652173;