8-69811789-T-C

Variant names:

• chr8-69811789-T-C
• rs10504460
• NM_030958.3:c.907+19978A>G

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+19978A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 152,276 control chromosomes in the GnomAD database, including 760 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 0.095 (760 hom., cov: 32)
• Consequence: SLCO5A1 NM_030958.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO5A1	NM_030958.3	c.907+19978A>G		intron_variant	Intron 2 of 9	ENST00000260126.9	NP_112220.2
SLCO5A1	NM_001146009.1	c.907+19978A>G		intron_variant	Intron 1 of 7		NP_001139481.1
SLCO5A1	NM_001146008.2	c.907+19978A>G		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+19978A>G		intron_variant	Intron 2 of 9	1	NM_030958.3	ENSP00000260126.3

Frequencies

GnomAD3 genomes AF: 0.0951 AC: 14466 AN: 152158 Hom.: 760 Cov.: 32

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0996

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.0950 AC: 14464 AN: 152276 Hom.: 760 Cov.: 32 AF XY: 0.0975 AC XY: 7263 AN XY: 74456

African (AFR) AF: 0.0921 AC: 3828 AN: 41548

American (AMR) AF: 0.0580 AC: 887 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5186

South Asian (SAS) AF: 0.0880 AC: 425 AN: 4828

European-Finnish (FIN) AF: 0.171 AC: 1809 AN: 10600

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0996 AC: 6775 AN: 68022

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0901 Hom.: 1104

Bravo AF: 0.0842

Asia WGS AF: 0.0380 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.26
DANN	Benign	0.66
PhyloP100		-0.086
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: rs10504460; hg19: chr8-70724024;