NM_145913.5:c.1526+1763G>A

Variant names:

• chr12-101164731-C-T
• rs2654993
• NM_145913.5:c.1526+1763G>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.1526+1763G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 152,264 control chromosomes in the GnomAD database, including 402 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 0.061 (402 hom., cov: 32)
• Consequence: SLC5A8 NM_145913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0847 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.1526+1763G>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.1526+1763G>A		intron	N/A	ENSP00000445340.2

Frequencies

GnomAD3 genomes AF: 0.0614 AC: 9340 AN: 152146 Hom.: 404 Cov.: 32

Gnomad AFR AF: 0.0142

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0664

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0863

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0613 AC: 9338 AN: 152264 Hom.: 402 Cov.: 32 AF XY: 0.0620 AC XY: 4612 AN XY: 74436

African (AFR) AF: 0.0142 AC: 591 AN: 41558

American (AMR) AF: 0.0661 AC: 1011 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3466

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0918 AC: 443 AN: 4826

European-Finnish (FIN) AF: 0.0768 AC: 814 AN: 10598

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0863 AC: 5868 AN: 68012

Other (OTH) AF: 0.0856 AC: 181 AN: 2114

Alfa AF: 0.0729 Hom.: 252

Bravo AF: 0.0572

Asia WGS AF: 0.0350 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		-0.040
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: rs2654993; hg19: chr12-101558509;