rs303169

Variant names:

• chr10-89435606-C-T
• rs303169
• NM_213606.4:c.1288+454G>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.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
• 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-AS1 (HGNC:51205): (SLC16A12 antisense RNA 1)

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 (AFR) allele frequency at 95% confidence interval = 0.823 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.1288+454G>A		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.1288+454G>A		intron	N/A	ENSP00000360855.4
	SLC16A12-AS1	ENST00000765073.1		n.99+3392C>T		intron	N/A

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

African (AFR) AF: 0.830 AC: 34419 AN: 41460

American (AMR) AF: 0.574 AC: 8771 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1983 AN: 3472

East Asian (EAS) AF: 0.792 AC: 4107 AN: 5184

South Asian (SAS) AF: 0.660 AC: 3181 AN: 4822

European-Finnish (FIN) AF: 0.486 AC: 5125 AN: 10556

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33246 AN: 67932

Other (OTH) AF: 0.620 AC: 1311 AN: 2114

Alfa AF: 0.529 Hom.: 29344

Bravo AF: 0.626

Asia WGS AF: 0.713 AC: 2475 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	0.36
DANN	Benign	0.48
PhyloP100		-0.65
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: rs303169; hg19: chr10-91195363;