rs2625154

Positions:

• chr12-101192544-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145913.5(SLC5A8):​c.692+1081C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,018 control chromosomes in the GnomAD database, including 5,745 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 0.26 (5745 hom., cov: 32)
• Consequence: SLC5A8 NM_145913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC5A8	NM_145913.5	c.692+1081C>T		intron_variant		ENST00000536262.3
SLC5A8	XM_017018910.3	c.692+1081C>T		intron_variant
SLC5A8	XR_007063055.1	n.1082+1081C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC5A8	ENST00000536262.3	c.692+1081C>T		intron_variant		1	NM_145913.5	P1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39972 AN: 151900 Hom.: 5733 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.263 AC: 40007 AN: 152018 Hom.: 5745 Cov.: 32 AF XY: 0.269 AC XY: 19968 AN XY: 74288

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.252

Alfa AF: 0.228 Hom.: 1746

Bravo AF: 0.261

Asia WGS AF: 0.323 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.54

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: rs2625154; hg19: chr12-101586322;