rs555044

chr12-226756-C-A

Variant summary

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

The NM_016615.5(SLC6A13):c.936-242G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 385,580 control chromosomes in the GnomAD database, including 16,326 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 0.31 (7652 hom., cov: 33)
  • Exomes 𝑓: 0.26 (8674 hom.)
• Consequence: SLC6A13 NM_016615.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A13	NM_016615.5	c.936-242G>T		intron_variant		ENST00000343164.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A13	ENST00000343164.9	c.936-242G>T		intron_variant		1	NM_016615.5	P1
SLC6A13	ENST00000445055.6	c.660-242G>T		intron_variant		2
SLC6A13	ENST00000542947.1	n.216G>T		non_coding_transcript_exon_variant	1/3	3
SLC6A13	ENST00000542379.1	n.220-3522G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46432 AN: 151966 Hom.: 7637 Cov.: 33

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.304

GnomAD4 exome AF: 0.259 AC: 60496 AN: 233494 Hom.: 8674 Cov.: 4 AF XY: 0.248 AC XY: 30368 AN XY: 122220

Gnomad4 AFR exome AF: 0.426

Gnomad4 AMR exome AF: 0.210

Gnomad4 ASJ exome AF: 0.278

Gnomad4 EAS exome AF: 0.374

Gnomad4 SAS exome AF: 0.119

Gnomad4 FIN exome AF: 0.314

Gnomad4 NFE exome AF: 0.265

Gnomad4 OTH exome AF: 0.269

GnomAD4 genome AF: 0.306 AC: 46483 AN: 152086 Hom.: 7652 Cov.: 33 AF XY: 0.304 AC XY: 22574 AN XY: 74354

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.306

Alfa AF: 0.264 Hom.: 7750

Bravo AF: 0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.6
Dann	Benign	0.83

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: rs555044; hg19: chr12-335922;