chr12-101206091-G-T

Variant names:

• chr12-101206091-G-T
• rs12580634
• NM_145913.5:c.352-1526C>A

Variant summary

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

The NM_145913.5(SLC5A8):​c.352-1526C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,090 control chromosomes in the GnomAD database, including 2,182 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 0.15 (2182 hom., cov: 32)
• Consequence: SLC5A8 NM_145913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540
• Publications: 2 publications found

Genes affected

SLC5A8 (HGNC:19119): (solute carrier family 5 member 8) SLC5A8 has been shown to transport iodide by a passive mechanism (Rodriguez et al., 2002 [PubMed 12107270]) and monocarboxylates and short-chain fatty acids by a sodium-coupled mechanism (Gopal et al., 2004 [PubMed 15322102]). In kidney, SLC5A8 functions as a high-affinity sodium-coupled lactate transporter involved in reabsorption of lactate and maintenance of blood lactate levels (Thangaraju et al., 2006 [PubMed 16873376]).[supplied by OMIM, Dec 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145913.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC5A8	NM_145913.5	MANE Select	c.352-1526C>A		intron	N/A	NP_666018.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC5A8	ENST00000536262.3	TSL:1 MANE Select	c.352-1526C>A		intron	N/A	ENSP00000445340.2

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22898 AN: 151972 Hom.: 2183 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.0998

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.151 AC: 22906 AN: 152090 Hom.: 2182 Cov.: 32 AF XY: 0.157 AC XY: 11651 AN XY: 74350

African (AFR) AF: 0.147 AC: 6092 AN: 41480

American (AMR) AF: 0.0996 AC: 1522 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2735 AN: 5168

South Asian (SAS) AF: 0.119 AC: 575 AN: 4828

European-Finnish (FIN) AF: 0.236 AC: 2490 AN: 10552

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8444 AN: 67984

Other (OTH) AF: 0.138 AC: 291 AN: 2116

Alfa AF: 0.133 Hom.: 1933

Bravo AF: 0.146

Asia WGS AF: 0.271 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.41
PhyloP100		0.54
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: rs12580634; hg19: chr12-101599869;