chr15-91994387-A-G

Variant names:

• chr15-91994387-A-G
• rs4932597
• NM_013272.4:c.646+77929A>G

Variant summary

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

The NM_013272.4(SLCO3A1):​c.646+77929A>G 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 152,116 control chromosomes in the GnomAD database, including 2,914 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 (2914 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.646+77929A>G		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.646+77929A>G		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.573+77929A>G		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.646+77929A>G		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6

Frequencies

GnomAD3 genomes AF: 0.178 AC: 26981 AN: 151998 Hom.: 2906 Cov.: 32

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.177 AC: 26990 AN: 152116 Hom.: 2914 Cov.: 32 AF XY: 0.184 AC XY: 13647 AN XY: 74336

African (AFR) AF: 0.0893 AC: 3708 AN: 41512

American (AMR) AF: 0.297 AC: 4534 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3472

East Asian (EAS) AF: 0.335 AC: 1733 AN: 5166

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4820

European-Finnish (FIN) AF: 0.232 AC: 2457 AN: 10572

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11983 AN: 67980

Other (OTH) AF: 0.182 AC: 383 AN: 2108

Alfa AF: 0.187 Hom.: 3799

Bravo AF: 0.181

Asia WGS AF: 0.275 AC: 957 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	9.1
DANN	Benign	0.87
PhyloP100		1.2
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: rs4932597; hg19: chr15-92537617;