Genetic Variant SLCO6A1:c.802+142A>G (chr5-102477534-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173488.5(SLCO6A1):c.802+142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 610,780 control chromosomes in the GnomAD database, including 124,768 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 0.64 ( 31037 hom., cov: 32)

Exomes 𝑓: 0.64 ( 93731 hom. )

Consequence

SLCO6A1
NM_173488.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.772

Variant links:

Genes affected

SLCO6A1 (HGNC:23613): (solute carrier organic anion transporter family member 6A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Predicted to be involved in sodium-independent organic anion transport. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLCO6A1 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=-0.65).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO6A1	NM_173488.5 link	c.802+142A>G		intron_variant	Intron 3 of 13	ENST00000506729.6	NP_775759.3	Q86UG4-1A0A140VJU7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO6A1	ENST00000506729.6 link	c.802+142A>G		intron_variant	Intron 3 of 13	1	NM_173488.5	ENSP00000421339.1		Q86UG4-1

Frequencies

GnomAD3 genomes

AF:

0.637

AC:

96777

AN:

151874

Hom.:

31015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.656

Gnomad AMI

AF:

0.688

Gnomad AMR

AF:

0.572

Gnomad ASJ

AF:

0.702

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.593

Gnomad FIN

AF:

0.732

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.639

Gnomad OTH

AF:

0.622

GnomAD4 exome

AF:

0.635

AC:

291375

AN:

458788

Hom.:

93731

AF XY:

0.635

AC XY:

149807

AN XY:

236100

show subpopulations

Gnomad4 AFR exome

AF:

0.672

Gnomad4 AMR exome

AF:

0.583

Gnomad4 ASJ exome

AF:

0.725

Gnomad4 EAS exome

AF:

0.461

Gnomad4 SAS exome

AF:

0.630

Gnomad4 FIN exome

AF:

0.710

Gnomad4 NFE exome

AF:

0.643

Gnomad4 OTH exome

AF:

0.629

GnomAD4 genome

AF:

0.637

AC:

96841

AN:

151992

Hom.:

31037

Cov.:

AF XY:

0.640

AC XY:

47551

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.656

Gnomad4 AMR

AF:

0.572

Gnomad4 ASJ

AF:

0.702

Gnomad4 EAS

AF:

0.458

Gnomad4 SAS

AF:

0.593

Gnomad4 FIN

AF:

0.732

Gnomad4 NFE

AF:

0.639

Gnomad4 OTH

AF:

0.617

Alfa

AF:

0.652

Hom.:

3990

Bravo

AF:

0.630

Asia WGS

AF:

0.525

AC:

1823

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.91

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