8-69733630-T-G

Variant names:

• chr8-69733630-T-G
• rs937086
• NM_030958.3:c.1423+4410A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030958.3(SLCO5A1):​c.1423+4410A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,966 control chromosomes in the GnomAD database, including 18,202 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 0.48 (18202 hom., cov: 32)
• Consequence: SLCO5A1 NM_030958.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO5A1	NM_030958.3	c.1423+4410A>C		intron_variant	Intron 5 of 9	ENST00000260126.9	NP_112220.2
SLCO5A1	NM_001146009.1	c.1258+21794A>C		intron_variant	Intron 3 of 7		NP_001139481.1
SLCO5A1	NM_001146008.2	c.1423+4410A>C		intron_variant	Intron 4 of 7		NP_001139480.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLCO5A1	ENST00000260126.9	c.1423+4410A>C		intron_variant	Intron 5 of 9	1	NM_030958.3	ENSP00000260126.3

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73483 AN: 151848 Hom.: 18192 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.484 AC: 73519 AN: 151966 Hom.: 18202 Cov.: 32 AF XY: 0.485 AC XY: 36026 AN XY: 74288

African (AFR) AF: 0.459 AC: 19002 AN: 41378

American (AMR) AF: 0.378 AC: 5777 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1616 AN: 3470

East Asian (EAS) AF: 0.342 AC: 1760 AN: 5152

South Asian (SAS) AF: 0.614 AC: 2956 AN: 4816

European-Finnish (FIN) AF: 0.543 AC: 5750 AN: 10580

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.514 AC: 34907 AN: 67962

Other (OTH) AF: 0.462 AC: 974 AN: 2106

Alfa AF: 0.342 Hom.: 878

Bravo AF: 0.465

Asia WGS AF: 0.497 AC: 1729 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	1.3
DANN	Benign	0.49
PhyloP100		-0.36
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: rs937086; hg19: chr8-70645865;