10-89433565-T-C

Position:

• chr10-89433565-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_213606.4(SLC16A12):​c.1289-239A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,176 control chromosomes in the GnomAD database, including 5,737 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (5737 hom., cov: 32)
• Consequence: SLC16A12 NM_213606.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.23

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 10-89433565-T-C is Benign according to our data. Variant chr10-89433565-T-C is described in ClinVar as [Benign]. Clinvar id is 1251034.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A12	NM_213606.4	c.1289-239A>G		intron_variant		ENST00000371790.5	NP_998771.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A12	ENST00000371790.5	c.1289-239A>G		intron_variant		2	NM_213606.4	ENSP00000360855.4

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40760 AN: 152058 Hom.: 5734 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.268 AC: 40780 AN: 152176 Hom.: 5737 Cov.: 32 AF XY: 0.265 AC XY: 19677 AN XY: 74392

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.283

Alfa AF: 0.267 Hom.: 1399

Bravo AF: 0.279

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 28, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.4
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs7090346; hg19: chr10-91193322;