rs12926788

Variant names:

• chr16-24868642-C-G
• rs12926788
• NM_001352248.3:c.208-1259C>G

Variant summary

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

The NM_001352248.3(SLC5A11):​c.208-1259C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 149,654 control chromosomes in the GnomAD database, including 4,149 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 0.23 (4149 hom., cov: 29)
• Consequence: SLC5A11 NM_001352248.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 8 publications found

Genes affected

SLC5A11 (HGNC:23091): (solute carrier family 5 member 11) Cotransporters, such as SLC5A11, represent a major class of proteins that make use of ion gradients to drive active transport for the cellular accumulation of nutrients, neurotransmitters, osmolytes, and ions Roll et al. (2002) [PubMed 12039040].[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC5A11	NM_001352248.3	c.208-1259C>G		intron_variant	Intron 4 of 16	ENST00000424767.7	NP_001339177.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC5A11	ENST00000424767.7	c.208-1259C>G		intron_variant	Intron 4 of 16	2	NM_001352248.3	ENSP00000416782.3

Frequencies

GnomAD3 genomes AF: 0.226 AC: 33848 AN: 149568 Hom.: 4137 Cov.: 29

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.227 AC: 33899 AN: 149654 Hom.: 4149 Cov.: 29 AF XY: 0.225 AC XY: 16364 AN XY: 72852

African (AFR) AF: 0.263 AC: 10738 AN: 40816

American (AMR) AF: 0.296 AC: 4443 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3464

East Asian (EAS) AF: 0.368 AC: 1870 AN: 5076

South Asian (SAS) AF: 0.200 AC: 952 AN: 4756

European-Finnish (FIN) AF: 0.155 AC: 1498 AN: 9642

Middle Eastern (MID) AF: 0.237 AC: 66 AN: 278

European-Non Finnish (NFE) AF: 0.194 AC: 13134 AN: 67650

Other (OTH) AF: 0.249 AC: 516 AN: 2072

Alfa AF: 0.209 Hom.: 442

Bravo AF: 0.242

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.3
DANN	Benign	0.65
PhyloP100		0.65
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: rs12926788; hg19: chr16-24879963;