rs7090346

Variant names:

• chr10-89433565-T-C
• rs7090346
• NM_213606.4:c.1289-239A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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 -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 VariationId 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.

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.1289-239A>G		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.1289-239A>G		intron	N/A	ENSP00000360855.4	Q6ZSM3
	SLC16A12	ENST00000899673.1		c.1289-239A>G		intron	N/A	ENSP00000569732.1
	SLC16A12	ENST00000899674.1		c.1289-239A>G		intron	N/A	ENSP00000569733.1

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

African (AFR) AF: 0.316 AC: 13122 AN: 41510

American (AMR) AF: 0.255 AC: 3891 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3472

East Asian (EAS) AF: 0.242 AC: 1252 AN: 5182

South Asian (SAS) AF: 0.103 AC: 495 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2271 AN: 10592

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17618 AN: 67998

Other (OTH) AF: 0.283 AC: 597 AN: 2110

Alfa AF: 0.269 Hom.: 1431

Bravo AF: 0.279

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.4
DANN	Benign	0.77
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7090346; hg19: chr10-91193322;