Variant chr15-92128494-TGGGATGGGGCAG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_013272.4(SLCO3A1):c.1512+23_1512+34del variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0142 in 1,611,622 control chromosomes in the GnomAD database, including 1,146 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.052 ( 562 hom., cov: 31)

Exomes 𝑓: 0.010 ( 584 hom. )

Consequence

SLCO3A1
NM_013272.4 splice_donor_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.479

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 15-92128494-TGGGATGGGGCAG-T is Benign according to our data. Variant chr15-92128494-TGGGATGGGGCAG-T is described in ClinVar as [Benign]. Clinvar id is 774718.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SLCO3A1	NM_013272.4 linkuse as main transcript	c.1512+23_1512+34del	splice_donor_region_variant, intron_variant	ENST00000318445.11
SLCO3A1	NM_001145044.1 linkuse as main transcript	c.1512+23_1512+34del	splice_donor_region_variant, intron_variant
SLCO3A1	NR_135775.2 linkuse as main transcript	n.1439+23_1439+34del	splice_donor_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO3A1	ENST00000318445.11 linkuse as main transcript	c.1512+23_1512+34del		splice_donor_region_variant, intron_variant		1	NM_013272.4	P1	Q9UIG8-1

Frequencies

GnomAD3 genomes

AF:

0.0515

AC:

7828

AN:

151944

Hom.:

557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0216

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.000774

Gnomad SAS

AF:

0.0123

Gnomad FIN

AF:

0.000850

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00612

Gnomad OTH

AF:

0.0354

GnomAD3 exomes

AF:

0.0170

AC:

4247

AN:

249232

Hom.:

241

AF XY:

0.0141

AC XY:

1903

AN XY:

134664

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.0100

Gnomad ASJ exome

AF:

0.00120

Gnomad EAS exome

AF:

0.000600

Gnomad SAS exome

AF:

0.0138

Gnomad FIN exome

AF:

0.00104

Gnomad NFE exome

AF:

0.00595

Gnomad OTH exome

AF:

0.00826

GnomAD4 exome

AF:

0.0103

AC:

15013

AN:

1459560

Hom.:

584

AF XY:

0.00990

AC XY:

7187

AN XY:

725960

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.0112

Gnomad4 ASJ exome

AF:

0.00184

Gnomad4 EAS exome

AF:

0.000277

Gnomad4 SAS exome

AF:

0.0136

Gnomad4 FIN exome

AF:

0.00115

Gnomad4 NFE exome

AF:

0.00587

Gnomad4 OTH exome

AF:

0.0154

GnomAD4 genome

AF:

0.0517

AC:

7867

AN:

152062

Hom.:

562

Cov.:

AF XY:

0.0503

AC XY:

3741

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.168

Gnomad4 AMR

AF:

0.0216

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.000775

Gnomad4 SAS

AF:

0.0123

Gnomad4 FIN

AF:

0.000850

Gnomad4 NFE

AF:

0.00612

Gnomad4 OTH

AF:

0.0355

Alfa

AF:

0.00834

Hom.:

Bravo

AF:

0.0589

Asia WGS

AF:

0.0300

AC:

104

AN:

3478

EpiCase

AF:

0.00601

EpiControl

AF:

0.00661

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over