dbSNP rs2238341: SLCO3A1:c.1754-955A>G (chr15-92161801-A-G) – 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.1754-955A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.065 ( 4 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

SLCO3A1
NM_013272.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76

Publications

3 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

new If you want to explore the variant's impact on the transcript NM_013272.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013272.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLCO3A1	NM_013272.4	MANE Select	c.1754-955A>G		intron	N/A	NP_037404.2	Q9UIG8-1
	SLCO3A1	NM_001145044.1		c.1754-955A>G		intron	N/A	NP_001138516.1	Q9UIG8-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLCO3A1	ENST00000318445.11	TSL:1 MANE Select	c.1754-955A>G	intron	N/A	ENSP00000320634.6	Q9UIG8-1
SLCO3A1	ENST00000424469.2	TSL:1	c.1754-955A>G	intron	N/A	ENSP00000387846.2	Q9UIG8-2
ENSG00000260661	ENST00000561674.1	TSL:1	n.186-4560T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0648

AC:

1131

AN:

17448

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0491

Gnomad AMI

AF:

0.00833

Gnomad AMR

AF:

0.0581

Gnomad ASJ

AF:

0.0640

Gnomad EAS

AF:

0.00430

Gnomad SAS

AF:

0.0607

Gnomad FIN

AF:

0.0684

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0821

Gnomad OTH

AF:

0.0714

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0647

AC:

1130

AN:

17470

Hom.:

Cov.:

AF XY:

0.0609

AC XY:

523

AN XY:

8588

show subpopulations

African (AFR)

AF:

0.0488

AC:

202

AN:

4138

American (AMR)

AF:

0.0583

AC:

AN:

1440

Ashkenazi Jewish (ASJ)

AF:

0.0640

AC:

AN:

328

East Asian (EAS)

AF:

0.00431

AC:

AN:

928

South Asian (SAS)

AF:

0.0613

AC:

AN:

914

European-Finnish (FIN)

AF:

0.0684

AC:

AN:

1272

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0819

AC:

659

AN:

8046

Other (OTH)

AF:

0.0702

AC:

AN:

228

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.409

Heterozygous variant carriers

112

149

186

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.465

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.3

(source)

DANN

Benign

0.16

PhyloP100

-1.8

Mutation Taster

=100/0

polymorphism

(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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over