10-89436445-T-C

Position:

• chr10-89436445-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_213606.4(SLC16A12):​c.1029-126A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0623 in 1,129,254 control chromosomes in the GnomAD database, including 4,592 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.11 (1889 hom., cov: 32)
  • Exomes 𝑓: 0.054 (2703 hom.)
• Consequence: SLC16A12 NM_213606.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.368

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 10-89436445-T-C is Benign according to our data. Variant chr10-89436445-T-C is described in ClinVar as [Benign]. Clinvar id is 1180132.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A12	NM_213606.4	c.1029-126A>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.1029-126A>G		intron_variant		2	NM_213606.4	ENSP00000360855	P1

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17050 AN: 152102 Hom.: 1867 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0538

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0898

GnomAD4 exome AF: 0.0545 AC: 53232 AN: 977034 Hom.: 2703 AF XY: 0.0575 AC XY: 28934 AN XY: 503180

Gnomad4 AFR exome AF: 0.288

Gnomad4 AMR exome AF: 0.0325

Gnomad4 ASJ exome AF: 0.0267

Gnomad4 EAS exome AF: 0.0222

Gnomad4 SAS exome AF: 0.149

Gnomad4 FIN exome AF: 0.0473

Gnomad4 NFE exome AF: 0.0401

Gnomad4 OTH exome AF: 0.0666

GnomAD4 genome AF: 0.112 AC: 17120 AN: 152220 Hom.: 1889 Cov.: 32 AF XY: 0.111 AC XY: 8252 AN XY: 74428

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.0537

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0409

Gnomad4 OTH AF: 0.0950

Alfa AF: 0.0555 Hom.: 151

Bravo AF: 0.117

Asia WGS AF: 0.130 AC: 450 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 27, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.56

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: rs2297312; hg19: chr10-91196202;