10-89519622-C-T

Variant names:

• chr10-89519622-C-T
• rs4933508
• NM_213606.4:c.-47+14879G>A

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+14879G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,520 control chromosomes in the GnomAD database, including 36,054 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 0.68 (36054 hom., cov: 28)
• Consequence: SLC16A12 NM_213606.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 2 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: AD, Unknown Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, PanelApp Australia

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A12	NM_213606.4	MANE Select	c.-47+14879G>A		intron	N/A	NP_998771.3	Q6ZSM3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A12	ENST00000371790.5	TSL:2 MANE Select	c.-47+14879G>A		intron	N/A	ENSP00000360855.4	Q6ZSM3
	SLC16A12	ENST00000899673.1		c.-47+16062G>A		intron	N/A	ENSP00000569732.1
	SLC16A12	ENST00000899674.1		c.-107-7479G>A		intron	N/A	ENSP00000569733.1

Frequencies

GnomAD3 genomes AF: 0.680 AC: 102988 AN: 151402 Hom.: 36012 Cov.: 28

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.680 AC: 103092 AN: 151520 Hom.: 36054 Cov.: 28 AF XY: 0.686 AC XY: 50769 AN XY: 74010

African (AFR) AF: 0.838 AC: 34599 AN: 41310

American (AMR) AF: 0.692 AC: 10528 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3466

East Asian (EAS) AF: 0.840 AC: 4319 AN: 5142

South Asian (SAS) AF: 0.691 AC: 3296 AN: 4770

European-Finnish (FIN) AF: 0.675 AC: 7067 AN: 10476

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39509 AN: 67848

Other (OTH) AF: 0.627 AC: 1317 AN: 2100

Alfa AF: 0.608 Hom.: 92828

Bravo AF: 0.689

Asia WGS AF: 0.732 AC: 2544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.6
DANN	Benign	0.89
PhyloP100		-0.15
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: rs4933508; hg19: chr10-91279379;