10-89519622-C-T

Position:

• chr10-89519622-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.-47+14879G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,520 control chromosomes in the GnomAD database, including 36,054 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 0.68 (36054 hom., cov: 28)
• Consequence: SLC16A12 NM_213606.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A12	NM_213606.4	c.-47+14879G>A		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+14879G>A		intron_variant		2	NM_213606.4	ENSP00000360855	P1
SLC16A12	ENST00000475682.1	c.-47+36260G>A		intron_variant		3		ENSP00000436965

Frequencies

GnomAD3 genomes AF: 0.680 AC: 102988 AN: 151402 Hom.: 36012 Cov.: 28

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.680 AC: 103092 AN: 151520 Hom.: 36054 Cov.: 28 AF XY: 0.686 AC XY: 50769 AN XY: 74010

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.627

Alfa AF: 0.588 Hom.: 36185

Bravo AF: 0.689

Asia WGS AF: 0.732 AC: 2544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.6
DANN	Benign	0.89

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: rs4933508; hg19: chr10-91279379;