rs10509574

Positions:

• chr10-89504532-C-G

Variant summary

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

The NM_213606.4(SLC16A12):​c.-47+29969G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0489 in 152,120 control chromosomes in the GnomAD database, including 369 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 0.049 (369 hom., cov: 32)
• Consequence: SLC16A12 NM_213606.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

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 = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A12	NM_213606.4	c.-47+29969G>C		intron_variant		ENST00000371790.5	NP_998771.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A12	ENST00000371790.5	c.-47+29969G>C		intron_variant		2	NM_213606.4	ENSP00000360855	P1
SLC16A12	ENST00000475682.1	c.-46-41908G>C		intron_variant		3		ENSP00000436965

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7414 AN: 152002 Hom.: 366 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0215

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0387

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

GnomAD4 genome AF: 0.0489 AC: 7438 AN: 152120 Hom.: 369 Cov.: 32 AF XY: 0.0506 AC XY: 3761 AN XY: 74344

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0214

Gnomad4 ASJ AF: 0.0231

Gnomad4 EAS AF: 0.0100

Gnomad4 SAS AF: 0.0123

Gnomad4 FIN AF: 0.0895

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0383

Alfa AF: 0.0334 Hom.: 18

Bravo AF: 0.0471

Asia WGS AF: 0.0270 AC: 93 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	1.4
DANN	Benign	0.36

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: rs10509574; hg19: chr10-91264289;