Variant rs312457 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_201566.3(SLC16A13):c.343+204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.968 in 614,950 control chromosomes in the GnomAD database, including 289,191 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 0.94 ( 67806 hom., cov: 31)

Exomes 𝑓: 0.98 ( 221385 hom. )

Consequence

SLC16A13
NM_201566.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.05

Variant links:

Genes affected

SLC16A13 (HGNC:31037): (solute carrier family 16 member 13) Predicted to enable monocarboxylic acid transmembrane transporter activity. Predicted to be involved in monocarboxylic acid transport. Located in Golgi apparatus and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

SLC16A13 links:

SLC16A13 (HGNC:):

SLC16A13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A13	NM_201566.3 linkuse as main transcript	c.343+204G>A		intron_variant		ENST00000308027.7	NP_963860.1	Q7RTY0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A13	ENST00000308027.7 linkuse as main transcript	c.343+204G>A		intron_variant		1	NM_201566.3	ENSP00000309751.6		Q7RTY0
SLC16A13	ENST00000575844.1 linkuse as main transcript	n.*10G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.942

AC:

143121

AN:

151912

Hom.:

67766

Cov.:

show subpopulations

Gnomad AFR

AF:

0.883

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.834

Gnomad ASJ

AF:

0.991

Gnomad EAS

AF:

0.903

Gnomad SAS

AF:

0.991

Gnomad FIN

AF:

0.979

Gnomad MID

AF:

0.991

Gnomad NFE

AF:

0.992

Gnomad OTH

AF:

0.948

GnomAD4 exome

AF:

0.977

AC:

452159

AN:

462918

Hom.:

221385

Cov.:

AF XY:

0.978

AC XY:

234993

AN XY:

240164

show subpopulations

Gnomad4 AFR exome

AF:

0.881

Gnomad4 AMR exome

AF:

0.769

Gnomad4 ASJ exome

AF:

0.988

Gnomad4 EAS exome

AF:

0.911

Gnomad4 SAS exome

AF:

0.996

Gnomad4 FIN exome

AF:

0.983

Gnomad4 NFE exome

AF:

0.992

Gnomad4 OTH exome

AF:

0.970

GnomAD4 genome

AF:

0.942

AC:

143219

AN:

152032

Hom.:

67806

Cov.:

AF XY:

0.941

AC XY:

69923

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.883

Gnomad4 AMR

AF:

0.834

Gnomad4 ASJ

AF:

0.991

Gnomad4 EAS

AF:

0.903

Gnomad4 SAS

AF:

0.991

Gnomad4 FIN

AF:

0.979

Gnomad4 NFE

AF:

0.992

Gnomad4 OTH

AF:

0.949

Alfa

AF:

0.967

Hom.:

11200

Bravo

AF:

0.923

Asia WGS

AF:

0.944

AC:

3285

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.50

DANN

Benign

0.78

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over