rs6472483

chr8-69717131-C-T

Variant summary

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

The NM_030958.3(SLCO5A1):c.1424-11902G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,966 control chromosomes in the GnomAD database, including 9,181 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 0.33 (9181 hom., cov: 32)
• Consequence: SLCO5A1 NM_030958.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

Genes affected

SLCO5A1 (HGNC:19046): (solute carrier organic anion transporter family member 5A1) Predicted to enable sodium-independent organic anion transmembrane transporter activity. Predicted to be involved in sodium-independent organic anion transport. Located in intracellular membrane-bounded organelle and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLCO5A1	NM_030958.3	c.1424-11902G>A		intron_variant		ENST00000260126.9
LOC105375889	XR_929026.3	n.162+2207C>T		intron_variant, non_coding_transcript_variant
SLCO5A1	NM_001146008.2	c.1424-11902G>A		intron_variant
SLCO5A1	NM_001146009.1	c.1259-11902G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO5A1	ENST00000260126.9	c.1424-11902G>A		intron_variant		1	NM_030958.3	P1
	ENST00000533344.1	n.506+2207C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50050 AN: 151846 Hom.: 9182 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.329 AC: 50047 AN: 151966 Hom.: 9181 Cov.: 32 AF XY: 0.329 AC XY: 24412 AN XY: 74254

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.344

Alfa AF: 0.362 Hom.: 4275

Bravo AF: 0.311

Asia WGS AF: 0.324 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.62

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: rs6472483; hg19: chr8-70629366; COSMIC: COSV52657746;