dbSNP rs9302356: SLCO3A1:c.*1544T>C (chr15-92164679-T-C) – 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.*1544T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 984,790 control chromosomes in the GnomAD database, including 197,796 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 ( 29628 hom., cov: 32)

Exomes 𝑓: 0.63 ( 168168 hom. )

Consequence

SLCO3A1
NM_013272.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.330

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:

Genome browser will be placed here

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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO3A1	NM_013272.4 link	c.*1544T>C		3_prime_UTR_variant	Exon 10 of 10	ENST00000318445.11	NP_037404.2	Q9UIG8-1
SLCO3A1	NM_001145044.1 link	c.1996+1681T>C		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.*1544T>C		3_prime_UTR_variant	Exon 10 of 10	1	NM_013272.4	ENSP00000320634.6		Q9UIG8-1

Frequencies

GnomAD3 genomes

AF:

0.619

AC:

93978

AN:

151830

Hom.:

29609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.641

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.656

Gnomad ASJ

AF:

0.691

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.473

Gnomad FIN

AF:

0.583

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.638

Gnomad OTH

AF:

0.654

GnomAD4 exome

AF:

0.634

AC:

528211

AN:

832842

Hom.:

168168

Cov.:

AF XY:

0.635

AC XY:

244175

AN XY:

384604

show subpopulations

African (AFR)

AF:

0.648

AC:

10223

AN:

15782

American (AMR)

AF:

0.654

AC:

644

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.692

AC:

3563

AN:

5150

East Asian (EAS)

AF:

0.232

AC:

841

AN:

3630

South Asian (SAS)

AF:

0.483

AC:

7945

AN:

16448

European-Finnish (FIN)

AF:

0.598

AC:

165

AN:

276

Middle Eastern (MID)

AF:

0.737

AC:

1196

AN:

1622

European-Non Finnish (NFE)

AF:

0.639

AC:

487059

AN:

761660

Other (OTH)

AF:

0.607

AC:

16575

AN:

27290

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

10048

20096

30144

40192

50240

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17586

35172

52758

70344

87930

<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:

0.619

AC:

94036

AN:

151948

Hom.:

29628

Cov.:

AF XY:

0.612

AC XY:

45434

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.641

AC:

26549

AN:

41414

American (AMR)

AF:

0.655

AC:

10006

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.691

AC:

2396

AN:

3468

East Asian (EAS)

AF:

0.240

AC:

1236

AN:

5152

South Asian (SAS)

AF:

0.475

AC:

2293

AN:

4826

European-Finnish (FIN)

AF:

0.583

AC:

6139

AN:

10530

Middle Eastern (MID)

AF:

0.759

AC:

223

AN:

294

European-Non Finnish (NFE)

AF:

0.638

AC:

43356

AN:

67982

Other (OTH)

AF:

0.648

AC:

1361

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1770

3540

5311

7081

8851

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

764

1528

2292

3056

3820

<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.:

36587

Bravo

AF:

0.633

Asia WGS

AF:

0.397

AC:

1387

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

0.36

(source)

DANN

Benign

0.33

PhyloP100

-0.33

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