rs7969185

Variant names:

• chr12-101162948-A-G
• rs7969185
• NM_145913.5:c.1527-871T>C

Variant summary

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

The NM_145913.5(SLC5A8):​c.1527-871T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,178 control chromosomes in the GnomAD database, including 4,150 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 0.21 (4150 hom., cov: 33)
• Consequence: SLC5A8 NM_145913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.937
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC5A8	NM_145913.5	MANE Select	c.1527-871T>C		intron	N/A	NP_666018.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC5A8	ENST00000536262.3	TSL:1 MANE Select	c.1527-871T>C		intron	N/A	ENSP00000445340.2	Q8N695
	SLC5A8	ENST00000957673.1		c.1461-871T>C		intron	N/A	ENSP00000627732.1
	SLC5A8	ENST00000957672.1		c.1341-871T>C		intron	N/A	ENSP00000627731.1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32396 AN: 152058 Hom.: 4140 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0975

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.213 AC: 32439 AN: 152178 Hom.: 4150 Cov.: 33 AF XY: 0.212 AC XY: 15752 AN XY: 74414

African (AFR) AF: 0.347 AC: 14409 AN: 41492

American (AMR) AF: 0.212 AC: 3239 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3470

East Asian (EAS) AF: 0.0979 AC: 507 AN: 5178

South Asian (SAS) AF: 0.160 AC: 770 AN: 4826

European-Finnish (FIN) AF: 0.162 AC: 1722 AN: 10602

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10669 AN: 68010

Other (OTH) AF: 0.200 AC: 423 AN: 2114

Alfa AF: 0.177 Hom.: 3863

Bravo AF: 0.222

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.62
PhyloP100		0.94
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: rs7969185; hg19: chr12-101556726;