rs10073892

Positions:

• chr5-102391066-T-C

Variant summary

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

The NM_173488.5(SLCO6A1):​c.1815-21A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,603,818 control chromosomes in the GnomAD database, including 57,670 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 0.21 (4580 hom., cov: 32)
  • Exomes 𝑓: 0.26 (53090 hom.)
• Consequence: SLCO6A1 NM_173488.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO6A1	NM_173488.5	c.1815-21A>G		intron_variant		ENST00000506729.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.1815-21A>G		intron_variant		1	NM_173488.5	P1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32547 AN: 151962 Hom.: 4584 Cov.: 32

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.240

GnomAD3 exomes AF: 0.244 AC: 60996 AN: 250326 Hom.: 8651 AF XY: 0.248 AC XY: 33474 AN XY: 135246

Gnomad AFR exome AF: 0.0454

Gnomad AMR exome AF: 0.163

Gnomad ASJ exome AF: 0.364

Gnomad EAS exome AF: 0.132

Gnomad SAS exome AF: 0.182

Gnomad FIN exome AF: 0.412

Gnomad NFE exome AF: 0.287

Gnomad OTH exome AF: 0.271

GnomAD4 exome AF: 0.263 AC: 381541 AN: 1451738 Hom.: 53090 Cov.: 29 AF XY: 0.262 AC XY: 189351 AN XY: 722998

Gnomad4 AFR exome AF: 0.0481

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.356

Gnomad4 EAS exome AF: 0.133

Gnomad4 SAS exome AF: 0.182

Gnomad4 FIN exome AF: 0.405

Gnomad4 NFE exome AF: 0.275

Gnomad4 OTH exome AF: 0.261

GnomAD4 genome AF: 0.214 AC: 32537 AN: 152080 Hom.: 4580 Cov.: 32 AF XY: 0.221 AC XY: 16387 AN XY: 74300

Gnomad4 AFR AF: 0.0514

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.241

Alfa AF: 0.270 Hom.: 11957

Bravo AF: 0.190

Asia WGS AF: 0.159 AC: 553 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
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: rs10073892; hg19: chr5-101726770;