Variant rs2238341 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO3A1	NM_013272.4 linkuse as main transcript	c.1754-955A>G		intron_variant		ENST00000318445.11	NP_037404.2
SLCO3A1	NM_001145044.1 linkuse as main transcript	c.1754-955A>G		intron_variant			NP_001138516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO3A1	ENST00000318445.11 linkuse as main transcript	c.1754-955A>G		intron_variant		1	NM_013272.4	ENSP00000320634	P1	Q9UIG8-1
	ENST00000561674.1 linkuse as main transcript	n.186-4560T>C		intron_variant, non_coding_transcript_variant		1

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:

GnomAD4 genome

AF:

0.0647

AC:

1130

AN:

17470

Hom.:

Cov.:

AF XY:

0.0609

AC XY:

523

AN XY:

8588

show subpopulations

Gnomad4 AFR

AF:

0.0488

Gnomad4 AMR

AF:

0.0583

Gnomad4 ASJ

AF:

0.0640

Gnomad4 EAS

AF:

0.00431

Gnomad4 SAS

AF:

0.0613

Gnomad4 FIN

AF:

0.0684

Gnomad4 NFE

AF:

0.0819

Gnomad4 OTH

AF:

0.0702

Alfa

AF:

0.465

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.3

DANN

Benign

0.16

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over