rs11746217

chr5-102459786-A-Gchr5-102459786-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.900-9T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 1,552,550 control chromosomes in the GnomAD database, including 330,201 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 0.65 (31865 hom., cov: 30)
  • Exomes 𝑓: 0.65 (298336 hom.)
• Consequence: SLCO6A1 NM_173488.5 splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.00008920
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO6A1	NM_173488.5	c.900-9T>C		splice_polypyrimidine_tract_variant, intron_variant		ENST00000506729.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO6A1	ENST00000506729.6	c.900-9T>C		splice_polypyrimidine_tract_variant, intron_variant		1	NM_173488.5	P1

Frequencies

GnomAD3 genomes AF: 0.647 AC: 97855 AN: 151322 Hom.: 31842 Cov.: 30

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.629

GnomAD3 exomes AF: 0.642 AC: 125218 AN: 195130 Hom.: 40921 AF XY: 0.642 AC XY: 68815 AN XY: 107240

Gnomad AFR exome AF: 0.671

Gnomad AMR exome AF: 0.576

Gnomad ASJ exome AF: 0.731

Gnomad EAS exome AF: 0.476

Gnomad SAS exome AF: 0.605

Gnomad FIN exome AF: 0.720

Gnomad NFE exome AF: 0.661

Gnomad OTH exome AF: 0.632

GnomAD4 exome AF: 0.650 AC: 910304 AN: 1401108 Hom.: 298336 Cov.: 31 AF XY: 0.648 AC XY: 452018 AN XY: 697256

Gnomad4 AFR exome AF: 0.674

Gnomad4 AMR exome AF: 0.576

Gnomad4 ASJ exome AF: 0.723

Gnomad4 EAS exome AF: 0.458

Gnomad4 SAS exome AF: 0.606

Gnomad4 FIN exome AF: 0.714

Gnomad4 NFE exome AF: 0.657

Gnomad4 OTH exome AF: 0.638

GnomAD4 genome AF: 0.647 AC: 97921 AN: 151442 Hom.: 31865 Cov.: 30 AF XY: 0.648 AC XY: 47934 AN XY: 73946

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.624

Alfa AF: 0.647 Hom.: 49878

Bravo AF: 0.640

Asia WGS AF: 0.522 AC: 1810 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.7
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000089
dbscSNV1_RF	Benign	0.038
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: rs11746217; hg19: chr5-101795490;