NM_030958.3:c.908-6873C>T

Variant names:

• chr8-69768748-G-A
• rs10090896
• NM_030958.3:c.908-6873C>T

Variant summary

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

The NM_030958.3(SLCO5A1):​c.908-6873C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,936 control chromosomes in the GnomAD database, including 6,546 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 0.25 (6546 hom., cov: 31)
• Consequence: SLCO5A1 NM_030958.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLCO5A1	NM_030958.3	c.908-6873C>T		intron_variant	Intron 2 of 9	ENST00000260126.9	NP_112220.2
SLCO5A1	NM_001146009.1	c.908-6873C>T		intron_variant	Intron 1 of 7		NP_001139481.1
SLCO5A1	NM_001146008.2	c.908-6873C>T		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.908-6873C>T		intron_variant	Intron 2 of 9	1	NM_030958.3	ENSP00000260126.3

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38159 AN: 151818 Hom.: 6527 Cov.: 31

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0839

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.252 AC: 38221 AN: 151936 Hom.: 6546 Cov.: 31 AF XY: 0.249 AC XY: 18517 AN XY: 74246

African (AFR) AF: 0.488 AC: 20189 AN: 41384

American (AMR) AF: 0.169 AC: 2578 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3464

East Asian (EAS) AF: 0.0838 AC: 433 AN: 5170

South Asian (SAS) AF: 0.256 AC: 1229 AN: 4806

European-Finnish (FIN) AF: 0.173 AC: 1833 AN: 10578

Middle Eastern (MID) AF: 0.190 AC: 55 AN: 290

European-Non Finnish (NFE) AF: 0.158 AC: 10715 AN: 67948

Other (OTH) AF: 0.211 AC: 444 AN: 2108

Alfa AF: 0.185 Hom.: 5842

Bravo AF: 0.258

Asia WGS AF: 0.211 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.22
PhyloP100		-0.57
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: rs10090896; hg19: chr8-70680983;