rs12926788

chr16-24868642-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC5A11	NM_001352248.3	c.208-1259C>G		intron_variant		ENST00000424767.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC5A11	ENST00000424767.7	c.208-1259C>G		intron_variant		2	NM_001352248.3	P1

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

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.249

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

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: rs12926788; hg19: chr16-24879963;