rs6472483

Variant names:

• chr8-69717131-C-T
• rs6472483
• NM_030958.3:c.1424-11902G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000254557 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLCO5A1	NM_030958.3	c.1424-11902G>A		intron_variant	Intron 5 of 9	ENST00000260126.9	NP_112220.2
SLCO5A1	NM_001146009.1	c.1259-11902G>A		intron_variant	Intron 3 of 7		NP_001139481.1
SLCO5A1	NM_001146008.2	c.1424-11902G>A		intron_variant	Intron 4 of 7		NP_001139480.1
LOC105375889	XR_929026.3	n.162+2207C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO5A1	ENST00000260126.9	c.1424-11902G>A		intron_variant	Intron 5 of 9	1	NM_030958.3	ENSP00000260126.3

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

African (AFR) AF: 0.179 AC: 7427 AN: 41444

American (AMR) AF: 0.277 AC: 4230 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1327 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1391 AN: 5176

South Asian (SAS) AF: 0.390 AC: 1882 AN: 4820

European-Finnish (FIN) AF: 0.402 AC: 4225 AN: 10520

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28237 AN: 67942

Other (OTH) AF: 0.344 AC: 725 AN: 2110

Alfa AF: 0.351 Hom.: 6439

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
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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