NM_013272.4:c.646+12642C>T

Variant names:

• chr15-91929100-C-T
• rs7175643
• NM_013272.4:c.646+12642C>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.646+12642C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,084 control chromosomes in the GnomAD database, including 3,953 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 0.22 (3953 hom., cov: 32)
• Consequence: SLCO3A1 NM_013272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4	c.646+12642C>T		intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1	c.646+12642C>T		intron_variant	Intron 2 of 10		NP_001138516.1
SLCO3A1	NR_135775.2	n.573+12642C>T		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11	c.646+12642C>T		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6
SLCO3A1	ENST00000424469.2	c.646+12642C>T		intron_variant	Intron 2 of 10	1		ENSP00000387846.2
SLCO3A1	ENST00000555769.5	n.541+12642C>T		intron_variant	Intron 2 of 10	1
SLCO3A1	ENST00000553653.5	n.832+12642C>T		intron_variant	Intron 2 of 8	5

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34115 AN: 151966 Hom.: 3954 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.224 AC: 34102 AN: 152084 Hom.: 3953 Cov.: 32 AF XY: 0.219 AC XY: 16317 AN XY: 74352

African (AFR) AF: 0.221 AC: 9151 AN: 41482

American (AMR) AF: 0.176 AC: 2698 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1079 AN: 5174

South Asian (SAS) AF: 0.216 AC: 1043 AN: 4822

European-Finnish (FIN) AF: 0.177 AC: 1870 AN: 10576

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

European-Non Finnish (NFE) AF: 0.250 AC: 16972 AN: 67958

Other (OTH) AF: 0.225 AC: 474 AN: 2108

Alfa AF: 0.238 Hom.: 1837

Bravo AF: 0.226

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.80
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: rs7175643; hg19: chr15-92472330;