rs10062613

chr5-102390279-C-T

Variant summary

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

The NM_173488.5(SLCO6A1):c.1879+702G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 151,978 control chromosomes in the GnomAD database, including 30,346 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 0.63 (30346 hom., cov: 31)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO6A1	NM_173488.5	c.1879+702G>A		intron_variant		ENST00000506729.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.1879+702G>A		intron_variant		1	NM_173488.5	P1

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95583 AN: 151860 Hom.: 30327 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.629 AC: 95644 AN: 151978 Hom.: 30346 Cov.: 31 AF XY: 0.632 AC XY: 46937 AN XY: 74276

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.617

Alfa AF: 0.653 Hom.: 4016

Bravo AF: 0.619

Asia WGS AF: 0.526 AC: 1824 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.7
Dann	Benign	0.31

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: rs10062613; hg19: chr5-101725983; COSMIC: COSV65807106;