rs476646

chr12-227968-T-C

Variant summary

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

The NM_016615.5(SLC6A13):c.832-300A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,890 control chromosomes in the GnomAD database, including 23,107 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 0.53 (23107 hom., cov: 31)
• Consequence: SLC6A13 NM_016615.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

Genes affected

SLC6A13 (HGNC:11046): (solute carrier family 6 member 13) Enables amino acid transmembrane transporter activity and monocarboxylic acid transmembrane transporter activity. Involved in amino acid import across plasma membrane and monocarboxylic acid transport. Located in extracellular exosome. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A13	NM_016615.5	c.832-300A>G		intron_variant		ENST00000343164.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A13	ENST00000343164.9	c.832-300A>G		intron_variant		1	NM_016615.5	P1
SLC6A13	ENST00000445055.6	c.556-300A>G		intron_variant		2
SLC6A13	ENST00000542379.1	n.220-4734A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81057 AN: 151772 Hom.: 23072 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.534 AC: 81139 AN: 151890 Hom.: 23107 Cov.: 31 AF XY: 0.534 AC XY: 39680 AN XY: 74254

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.514

Alfa AF: 0.474 Hom.: 3747

Bravo AF: 0.548

Asia WGS AF: 0.572 AC: 1989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.9
Dann	Benign	0.37

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: rs476646; hg19: chr12-337134;