rs17479692

chr10-89528702-T-G

Variant summary

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

The NM_213606.4(SLC16A12):c.-47+5799A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 152,226 control chromosomes in the GnomAD database, including 790 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 0.093 (790 hom., cov: 32)
• Consequence: SLC16A12 NM_213606.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

Genes affected

SLC16A12 (HGNC:23094): (solute carrier family 16 member 12) This gene encodes a transmembrane transporter that likely plays a role in monocarboxylic acid transport. A mutation in this gene has been associated with juvenile cataracts with microcornea and renal glucosuria. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A12	NM_213606.4	c.-47+5799A>C		intron_variant		ENST00000371790.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A12	ENST00000371790.5	c.-47+5799A>C		intron_variant		2	NM_213606.4	P1
SLC16A12	ENST00000475682.1	c.-47+27180A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14119 AN: 152108 Hom.: 789 Cov.: 32

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0800

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.0598

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.0927 AC: 14118 AN: 152226 Hom.: 790 Cov.: 32 AF XY: 0.0938 AC XY: 6982 AN XY: 74424

Gnomad4 AFR AF: 0.0288

Gnomad4 AMR AF: 0.0799

Gnomad4 ASJ AF: 0.0757

Gnomad4 EAS AF: 0.0980

Gnomad4 SAS AF: 0.0609

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.0947

Alfa AF: 0.110 Hom.: 489

Bravo AF: 0.0840

Asia WGS AF: 0.0810 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.4
Dann	Benign	0.78

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: rs17479692; hg19: chr10-91288459;