Genetic Variant SLCO3A1:c.646+25149G>T (chr15-91941607-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013272.4(SLCO3A1):c.646+25149G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0689 in 455,534 control chromosomes in the GnomAD database, including 1,325 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 0.075 ( 490 hom., cov: 32)

Exomes 𝑓: 0.066 ( 835 hom. )

Consequence

SLCO3A1
NM_013272.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.156

Publications

7 publications found

Variant links:

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]

SLCO3A1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4 link	c.646+25149G>T	intron_variant	Intron 2 of 9	ENST00000318445.11	NP_037404.2	Q9UIG8-1
SLCO3A1	NM_001145044.1 link	c.646+25149G>T	intron_variant	Intron 2 of 10		NP_001138516.1	Q9UIG8-2
SLCO3A1	NR_135775.2 link	n.573+25149G>T	intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11 link	c.646+25149G>T		intron_variant	Intron 2 of 9	1	NM_013272.4	ENSP00000320634.6		Q9UIG8-1

Frequencies

GnomAD3 genomes

AF:

0.0748

AC:

11373

AN:

152076

Hom.:

488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0686

Gnomad AMI

AF:

0.0976

Gnomad AMR

AF:

0.0447

Gnomad ASJ

AF:

0.0331

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0214

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0897

Gnomad OTH

AF:

0.0712

GnomAD2 exomes

AF:

0.0550

AC:

7032

AN:

127750

AF XY:

0.0532

show subpopulations

Gnomad AFR exome

AF:

0.0687

Gnomad AMR exome

AF:

0.0327

Gnomad ASJ exome

AF:

0.0422

Gnomad EAS exome

AF:

0.000767

Gnomad FIN exome

AF:

0.116

Gnomad NFE exome

AF:

0.0872

Gnomad OTH exome

AF:

0.0576

GnomAD4 exome

AF:

0.0658

AC:

19970

AN:

303340

Hom.:

835

Cov.:

AF XY:

0.0610

AC XY:

10537

AN XY:

172780

show subpopulations

African (AFR)

AF:

0.0664

AC:

570

AN:

8590

American (AMR)

AF:

0.0334

AC:

910

AN:

27216

Ashkenazi Jewish (ASJ)

AF:

0.0411

AC:

443

AN:

10774

East Asian (EAS)

AF:

0.00141

AC:

AN:

9198

South Asian (SAS)

AF:

0.0225

AC:

1340

AN:

59650

European-Finnish (FIN)

AF:

0.118

AC:

1462

AN:

12356

Middle Eastern (MID)

AF:

0.0227

AC:

AN:

2774

European-Non Finnish (NFE)

AF:

0.0894

AC:

14178

AN:

158598

Other (OTH)

AF:

0.0699

AC:

991

AN:

14184

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

927

1853

2780

3706

4633

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

168

224

280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0749

AC:

11400

AN:

152194

Hom.:

490

Cov.:

AF XY:

0.0727

AC XY:

5412

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0687

AC:

2853

AN:

41518

American (AMR)

AF:

0.0447

AC:

684

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.0331

AC:

115

AN:

3472

East Asian (EAS)

AF:

0.00174

AC:

AN:

5180

South Asian (SAS)

AF:

0.0218

AC:

105

AN:

4818

European-Finnish (FIN)

AF:

0.121

AC:

1279

AN:

10572

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0897

AC:

6100

AN:

68006

Other (OTH)

AF:

0.0752

AC:

159

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

531

1061

1592

2122

2653

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0797

Hom.:

1255

Bravo

AF:

0.0684

Asia WGS

AF:

0.0510

AC:

178

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.7

(source)

DANN

Benign

0.50

PhyloP100

0.16

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over