chr10-89528702-T-G

Variant names:

• chr10-89528702-T-G
• rs17479692
• NM_213606.4:c.-47+5799A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

SLC16A12 Gene-Disease associations (from GenCC):

• juvenile cataract-microcornea-renal glucosuria syndrome

  Inheritance: Unknown, AD Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Laboratory for Molecular Medicine, G2P, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_213606.4. 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
	SLC16A12	NM_213606.4	MANE Select	c.-47+5799A>C		intron	N/A	NP_998771.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A12	ENST00000371790.5	TSL:2 MANE Select	c.-47+5799A>C		intron	N/A	ENSP00000360855.4
	SLC16A12	ENST00000475682.1	TSL:3	c.-47+27180A>C		intron	N/A	ENSP00000436965.1

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

African (AFR) AF: 0.0288 AC: 1197 AN: 41540

American (AMR) AF: 0.0799 AC: 1222 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0757 AC: 263 AN: 3472

East Asian (EAS) AF: 0.0980 AC: 508 AN: 5184

South Asian (SAS) AF: 0.0609 AC: 294 AN: 4826

European-Finnish (FIN) AF: 0.165 AC: 1749 AN: 10594

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8555 AN: 68002

Other (OTH) AF: 0.0947 AC: 200 AN: 2112

Alfa AF: 0.110 Hom.: 696

Bravo AF: 0.0840

Asia WGS AF: 0.0810 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.78
PhyloP100		0.084
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: rs17479692; hg19: chr10-91288459;