rs499368

chr12-211754-T-Achr12-211754-T-C

Variant summary

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

The NM_001122848.3(SLC6A12):c.-58+272A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 152,018 control chromosomes in the GnomAD database, including 20,122 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 0.51 (20122 hom., cov: 33)
• Consequence: SLC6A12 NM_001122848.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

SLC6A12 (HGNC:11045): (solute carrier family 6 member 12) Enables monocarboxylic acid transmembrane transporter activity. Involved in monocarboxylic acid transport. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. Predicted to be active in neuron projection. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A12	NM_001122848.3	c.-58+272A>T		intron_variant		ENST00000684302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A12	ENST00000684302.1	c.-58+272A>T		intron_variant			NM_001122848.3	P1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77749 AN: 151900 Hom.: 20113 Cov.: 33

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.512 AC: 77801 AN: 152018 Hom.: 20122 Cov.: 33 AF XY: 0.510 AC XY: 37861 AN XY: 74292

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.499

Alfa AF: 0.353 Hom.: 840

Bravo AF: 0.515

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.10
Dann	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs499368; hg19: chr12-320920;