rs10504461

Variant names:

• chr8-69813052-C-T
• rs10504461
• NM_030958.3:c.907+18715G>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.907+18715G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0623 in 151,890 control chromosomes in the GnomAD database, including 449 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 0.062 (449 hom., cov: 32)
• Consequence: SLCO5A1 NM_030958.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 1 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO5A1	NM_030958.3	c.907+18715G>A		intron_variant	Intron 2 of 9	ENST00000260126.9	NP_112220.2
SLCO5A1	NM_001146009.1	c.907+18715G>A		intron_variant	Intron 1 of 7		NP_001139481.1
SLCO5A1	NM_001146008.2	c.907+18715G>A		intron_variant	Intron 1 of 7		NP_001139480.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO5A1	ENST00000260126.9	c.907+18715G>A		intron_variant	Intron 2 of 9	1	NM_030958.3	ENSP00000260126.3

Frequencies

GnomAD3 genomes AF: 0.0623 AC: 9456 AN: 151772 Hom.: 447 Cov.: 32

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.0470

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

GnomAD4 genome AF: 0.0623 AC: 9463 AN: 151890 Hom.: 449 Cov.: 32 AF XY: 0.0626 AC XY: 4650 AN XY: 74242

African (AFR) AF: 0.0240 AC: 990 AN: 41318

American (AMR) AF: 0.0910 AC: 1388 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0649 AC: 225 AN: 3468

East Asian (EAS) AF: 0.253 AC: 1305 AN: 5168

South Asian (SAS) AF: 0.0839 AC: 404 AN: 4818

European-Finnish (FIN) AF: 0.0495 AC: 523 AN: 10568

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0652 AC: 4430 AN: 67984

Other (OTH) AF: 0.0474 AC: 100 AN: 2108

Alfa AF: 0.0626 Hom.: 391

Bravo AF: 0.0641

Asia WGS AF: 0.129 AC: 448 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.81
DANN	Benign	0.42
PhyloP100		0.011
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: rs10504461; hg19: chr8-70725287;