Variant 8-69672988-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_030958.3(SLCO5A1):c.2428C>T(p.Leu810Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.002 in 1,614,070 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0021 ( 5 hom. )

Consequence

SLCO5A1
NM_030958.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.13

Variant links:

Genes affected

SLCO5A1 (HGNC:19046): (solute carrier organic anion transporter family member 5A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Predicted to be involved in sodium-independent organic anion transport. Located in intracellular membrane-bounded organelle and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLCO5A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 8-69672988-G-A is Benign according to our data. Variant chr8-69672988-G-A is described in ClinVar as [Benign]. Clinvar id is 782750.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.13 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLCO5A1	NM_030958.3 linkuse as main transcript	c.2428C>T	p.Leu810Leu	synonymous_variant	10/10	ENST00000260126.9	NP_112220.2	Q9H2Y9-1B3KUC7
SLCO5A1	NM_001146009.1 linkuse as main transcript	c.2263C>T	p.Leu755Leu	synonymous_variant	8/8		NP_001139481.1	Q9H2Y9-2
SLCO5A1	NM_001146008.2 linkuse as main transcript	c.*299C>T		3_prime_UTR_variant	8/8		NP_001139480.1	Q9H2Y9-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLCO5A1	ENST00000260126.9 linkuse as main transcript	c.2428C>T	p.Leu810Leu	synonymous_variant	10/10	1	NM_030958.3	ENSP00000260126.3		Q9H2Y9-1

Frequencies

GnomAD3 genomes

AF:

0.00148

AC:

225

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000627

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000327

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00259

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00161

AC:

405

AN:

251362

Hom.:

AF XY:

0.00146

AC XY:

199

AN XY:

135852

show subpopulations

Gnomad AFR exome

AF:

0.000308

Gnomad AMR exome

AF:

0.000260

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000719

Gnomad FIN exome

AF:

0.00199

Gnomad NFE exome

AF:

0.00281

Gnomad OTH exome

AF:

0.00114

GnomAD4 exome

AF:

0.00206

AC:

3008

AN:

1461894

Hom.:

Cov.:

AF XY:

0.00203

AC XY:

1475

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.000201

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000672

Gnomad4 FIN exome

AF:

0.00148

Gnomad4 NFE exome

AF:

0.00250

Gnomad4 OTH exome

AF:

0.00121

GnomAD4 genome

AF:

0.00148

AC:

225

AN:

152176

Hom.:

Cov.:

AF XY:

0.00145

AC XY:

108

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.000627

Gnomad4 AMR

AF:

0.000327

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00259

Gnomad4 OTH

AF:

0.000478

Alfa

AF:

0.00180

Hom.:

Bravo

AF:

0.00138

EpiCase

AF:

0.00311

EpiControl

AF:

0.00219

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 23, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

3.8

DANN

Benign

0.69

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over