rs1452057

chr5-102453601-A-Gchr5-102453601-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173488.5(SLCO6A1):c.1131+4781T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,954 control chromosomes in the GnomAD database, including 31,016 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 (31016 hom., cov: 31)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO6A1	NM_173488.5	c.1131+4781T>C		intron_variant		ENST00000506729.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.1131+4781T>C		intron_variant		1	NM_173488.5	P1

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96736 AN: 151836 Hom.: 30994 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.621

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.637 AC: 96800 AN: 151954 Hom.: 31016 Cov.: 31 AF XY: 0.640 AC XY: 47523 AN XY: 74254

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.617

Alfa AF: 0.631 Hom.: 39105

Bravo AF: 0.629

Asia WGS AF: 0.525 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.4
Dann	Benign	0.53

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

Other links and lift over

dbSNP: rs1452057; hg19: chr5-101789305; COSMIC: COSV65807635;