Variant 10-59709780-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_194298.3(SLC16A9):c.-338A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,774 control chromosomes in the GnomAD database, including 48,126 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 0.79 ( 47924 hom., cov: 33)

Exomes 𝑓: 0.79 ( 202 hom. )

Consequence

SLC16A9
NM_194298.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.814

Variant links:

Genes affected

SLC16A9 (HGNC:23520): (solute carrier family 16 member 9) Predicted to enable monocarboxylic acid transmembrane transporter activity. Involved in urate metabolic process. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC16A9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A9	NM_194298.3 link	c.-338A>G		5_prime_UTR_variant	1/6	ENST00000395348.8	NP_919274.1	Q7RTY1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A9	ENST00000395348.8 link	c.-338A>G		5_prime_UTR_variant	1/6	5	NM_194298.3	ENSP00000378757.3		Q7RTY1
SLC16A9	ENST00000395347.1 link	c.-36-25453A>G		intron_variant		2		ENSP00000378756.1		Q7RTY1

Frequencies

GnomAD3 genomes

AF:

0.792

AC:

120356

AN:

152026

Hom.:

47874

Cov.:

show subpopulations

Gnomad AFR

AF:

0.765

Gnomad AMI

AF:

0.537

Gnomad AMR

AF:

0.826

Gnomad ASJ

AF:

0.803

Gnomad EAS

AF:

0.998

Gnomad SAS

AF:

0.849

Gnomad FIN

AF:

0.849

Gnomad MID

AF:

0.769

Gnomad NFE

AF:

0.776

Gnomad OTH

AF:

0.766

GnomAD4 exome

AF:

0.789

AC:

497

AN:

630

Hom.:

202

Cov.:

AF XY:

0.805

AC XY:

375

AN XY:

466

show subpopulations

Gnomad4 AFR exome

AF:

0.800

Gnomad4 AMR exome

AF:

0.929

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.833

Gnomad4 NFE exome

AF:

0.772

Gnomad4 OTH exome

AF:

0.821

GnomAD4 genome

AF:

0.792

AC:

120465

AN:

152144

Hom.:

47924

Cov.:

AF XY:

0.797

AC XY:

59321

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.765

Gnomad4 AMR

AF:

0.826

Gnomad4 ASJ

AF:

0.803

Gnomad4 EAS

AF:

0.998

Gnomad4 SAS

AF:

0.850

Gnomad4 FIN

AF:

0.849

Gnomad4 NFE

AF:

0.776

Gnomad4 OTH

AF:

0.768

Alfa

AF:

0.780

Hom.:

19014

Bravo

AF:

0.787

Asia WGS

AF:

0.922

AC:

3199

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.69

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