rs2053736

chr12-244088-C-T

Variant summary

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

The NM_016615.5(SLC6A13):c.203-275G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0522 in 152,300 control chromosomes in the GnomAD database, including 566 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 0.052 (566 hom., cov: 33)
• Consequence: SLC6A13 NM_016615.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A13	NM_016615.5	c.203-275G>A		intron_variant		ENST00000343164.9
SLC6A13	NM_001190997.3	c.203-6078G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A13	ENST00000343164.9	c.203-275G>A		intron_variant		1	NM_016615.5	P1

Frequencies

GnomAD3 genomes AF: 0.0521 AC: 7934 AN: 152182 Hom.: 563 Cov.: 33

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00297

Gnomad OTH AF: 0.0530

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

GnomAD4 genome AF: 0.0522 AC: 7948 AN: 152300 Hom.: 566 Cov.: 33 AF XY: 0.0562 AC XY: 4186 AN XY: 74482

Gnomad4 AFR AF: 0.0883

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.0406

Gnomad4 FIN AF: 0.0223

Gnomad4 NFE AF: 0.00297

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0438 Hom.: 66

Bravo AF: 0.0648

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.7
Dann	Benign	0.49

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: rs2053736; hg19: chr12-353254;