Genetic Variant SLCO3A1:c.*1938C>T (chr15-92165073-C-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.*1938C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 984,936 control chromosomes in the GnomAD database, including 195,314 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 0.62 ( 29343 hom., cov: 32)

Exomes 𝑓: 0.63 ( 165971 hom. )

Consequence

SLCO3A1
NM_013272.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.61

Publications

1 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:

ENSG00000260661 (HGNC:):

ENSG00000260661 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=-0.79).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4 link	c.*1938C>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000318445.11	NP_037404.2	Q9UIG8-1
SLCO3A1	NM_001145044.1 link	c.1996+2075C>T		intron_variant	Intron 10 of 10		NP_001138516.1	Q9UIG8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11 link	c.*1938C>T		3_prime_UTR_variant	Exon 10 of 10	1	NM_013272.4	ENSP00000320634.6		Q9UIG8-1

Frequencies

GnomAD3 genomes

AF:

0.616

AC:

93586

AN:

151944

Hom.:

29324

Cov.:

show subpopulations

Gnomad AFR

AF:

0.638

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.655

Gnomad ASJ

AF:

0.690

Gnomad EAS

AF:

0.242

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.584

Gnomad MID

AF:

0.741

Gnomad NFE

AF:

0.634

Gnomad OTH

AF:

0.651

GnomAD4 exome

AF:

0.630

AC:

524746

AN:

832874

Hom.:

165971

Cov.:

AF XY:

0.631

AC XY:

242557

AN XY:

384598

show subpopulations

African (AFR)

AF:

0.651

AC:

10270

AN:

15784

American (AMR)

AF:

0.651

AC:

641

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.691

AC:

3561

AN:

5152

East Asian (EAS)

AF:

0.233

AC:

844

AN:

3630

South Asian (SAS)

AF:

0.465

AC:

7655

AN:

16454

European-Finnish (FIN)

AF:

0.598

AC:

165

AN:

276

Middle Eastern (MID)

AF:

0.732

AC:

1186

AN:

1620

European-Non Finnish (NFE)

AF:

0.635

AC:

483967

AN:

761682

Other (OTH)

AF:

0.603

AC:

16457

AN:

27292

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

9740

19481

29221

38962

48702

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17530

35060

52590

70120

87650

<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:

0.616

AC:

93647

AN:

152062

Hom.:

29343

Cov.:

AF XY:

0.609

AC XY:

45239

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.638

AC:

26474

AN:

41484

American (AMR)

AF:

0.654

AC:

10000

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.690

AC:

2396

AN:

3470

East Asian (EAS)

AF:

0.242

AC:

1251

AN:

5168

South Asian (SAS)

AF:

0.457

AC:

2200

AN:

4812

European-Finnish (FIN)

AF:

0.584

AC:

6162

AN:

10552

Middle Eastern (MID)

AF:

0.759

AC:

223

AN:

294

European-Non Finnish (NFE)

AF:

0.634

AC:

43126

AN:

67976

Other (OTH)

AF:

0.645

AC:

1362

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1852

3703

5555

7406

9258

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

760

1520

2280

3040

3800

<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:

0.630

Hom.:

41780

Bravo

AF:

0.631

Asia WGS

AF:

0.388

AC:

1357

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.1

(source)

DANN

Benign

0.54

PhyloP100

1.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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