rs303169

Positions:

• chr10-89435606-C-T

Variant summary

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

The NM_213606.4(SLC16A12):​c.1288+454G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,018 control chromosomes in the GnomAD database, including 30,219 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 0.61 (30219 hom., cov: 31)
• Consequence: SLC16A12 NM_213606.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

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 (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A12	NM_213606.4	c.1288+454G>A		intron_variant		ENST00000371790.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A12	ENST00000371790.5	c.1288+454G>A		intron_variant		2	NM_213606.4	P1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92824 AN: 151900 Hom.: 30171 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.611 AC: 92926 AN: 152018 Hom.: 30219 Cov.: 31 AF XY: 0.613 AC XY: 45531 AN XY: 74330

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.620

Alfa AF: 0.519 Hom.: 20493

Bravo AF: 0.626

Asia WGS AF: 0.713 AC: 2475 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	0.36
DANN	Benign	0.48

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: rs303169; hg19: chr10-91195363;