chr12-101167185-C-T

Variant names:

• chr12-101167185-C-T
• rs164364
• NM_145913.5:c.1321-486G>A

Variant summary

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

The NM_145913.5(SLC5A8):​c.1321-486G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,940 control chromosomes in the GnomAD database, including 15,996 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 0.45 (15996 hom., cov: 33)
• Consequence: SLC5A8 NM_145913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC5A8	NM_145913.5	c.1321-486G>A		intron_variant	Intron 11 of 14	ENST00000536262.3	NP_666018.3
SLC5A8	XM_017018910.3	c.1321-323G>A		intron_variant	Intron 11 of 11		XP_016874399.1
SLC5A8	XR_007063055.1	n.1711-486G>A		intron_variant	Intron 11 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC5A8	ENST00000536262.3	c.1321-486G>A		intron_variant	Intron 11 of 14	1	NM_145913.5	ENSP00000445340.2

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68399 AN: 151822 Hom.: 15982 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.450 AC: 68446 AN: 151940 Hom.: 15996 Cov.: 33 AF XY: 0.455 AC XY: 33793 AN XY: 74234

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.436

Alfa AF: 0.405 Hom.: 5912

Bravo AF: 0.450

Asia WGS AF: 0.521 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.76
DANN	Benign	0.43

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: rs164364; hg19: chr12-101560963;