Genetic Variant NM_016615.5:c.936-242G>A (chr12-226756-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_016615.5(SLC6A13):c.936-242G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000854 in 234,088 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000085 ( 0 hom. )

Consequence

SLC6A13
NM_016615.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.492

Publications

0 publications found

Variant links:

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]

SLC6A13 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A13	NM_016615.5 link	c.936-242G>A		intron_variant	Intron 8 of 14	ENST00000343164.9	NP_057699.2	Q9NSD5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A13	ENST00000343164.9 link	c.936-242G>A		intron_variant	Intron 8 of 14	1	NM_016615.5	ENSP00000339260.4		Q9NSD5-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000854

AC:

AN:

234088

Hom.:

Cov.:

AF XY:

0.0000163

AC XY:

AN XY:

122524

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

6854

American (AMR)

AF:

0.00

AC:

AN:

9072

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6798

East Asian (EAS)

AF:

0.00

AC:

AN:

13566

South Asian (SAS)

AF:

0.0000351

AC:

AN:

28482

European-Finnish (FIN)

AF:

0.00

AC:

AN:

12070

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1004

European-Non Finnish (NFE)

AF:

0.00000698

AC:

AN:

143280

Other (OTH)

AF:

0.00

AC:

AN:

12962

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.6

(source)

DANN

Benign

0.97

PhyloP100

-0.49

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over