rs10774021

Variant names:

• chr12-240132-C-T
• rs10774021
• NM_016615.5:c.479-2122G>A

Variant summary

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

The NM_016615.5(SLC6A13):​c.479-2122G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,852 control chromosomes in the GnomAD database, including 25,529 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 0.57 (25529 hom., cov: 31)
• Consequence: SLC6A13 NM_016615.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A13	NM_016615.5	c.479-2122G>A		intron_variant	Intron 4 of 14	ENST00000343164.9	NP_057699.2
SLC6A13	NM_001190997.3	c.203-2122G>A		intron_variant	Intron 2 of 12		NP_001177926.1
SLC6A13	XM_047429420.1	c.-181-1789G>A		intron_variant	Intron 1 of 12		XP_047285376.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A13	ENST00000343164.9	c.479-2122G>A		intron_variant	Intron 4 of 14	1	NM_016615.5	ENSP00000339260.4

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86209 AN: 151734 Hom.: 25501 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.568 AC: 86280 AN: 151852 Hom.: 25529 Cov.: 31 AF XY: 0.566 AC XY: 41999 AN XY: 74238

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.557

Alfa AF: 0.625 Hom.: 67661

Bravo AF: 0.540

Asia WGS AF: 0.434 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.34

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: rs10774021; hg19: chr12-349298;