8-69811789-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLCO5A1	NM_030958.3	c.907+19978A>G		intron_variant		ENST00000260126.9
SLCO5A1	NM_001146008.2	c.907+19978A>G		intron_variant
SLCO5A1	NM_001146009.1	c.907+19978A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLCO5A1	ENST00000260126.9	c.907+19978A>G		intron_variant		1	NM_030958.3	P1

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

Gnomad4 AFR AF: 0.0921

Gnomad4 AMR AF: 0.0580

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0880

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.0996

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0901 Hom.: 866

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

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: rs10504460; hg19: chr8-70724024;