Genetic Variant SLC16A9:c.-338A>G (chr10-59709780-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

60 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC16A9	NM_194298.3 link	c.-338A>G		5_prime_UTR_variant	Exon 1 of 6	ENST00000395348.8	NP_919274.1	Q7RTY1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A9	ENST00000395348.8 link	c.-338A>G		5_prime_UTR_variant	Exon 1 of 6	5	NM_194298.3	ENSP00000378757.3		Q7RTY1
SLC16A9	ENST00000395347.1 link	c.-36-25453A>G		intron_variant	Intron 1 of 5	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

African (AFR)

AF:

0.800

AC:

AN:

American (AMR)

AF:

0.929

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AF:

0.750

AC:

AN:

European-Non Finnish (NFE)

AF:

0.772

AC:

412

AN:

534

Other (OTH)

AF:

0.821

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.792

AC:

120465

AN:

152144

Hom.:

47924

Cov.:

AF XY:

0.797

AC XY:

59321

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.765

AC:

31760

AN:

41528

American (AMR)

AF:

0.826

AC:

12631

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.803

AC:

2785

AN:

3470

East Asian (EAS)

AF:

0.998

AC:

5130

AN:

5138

South Asian (SAS)

AF:

0.850

AC:

4098

AN:

4820

European-Finnish (FIN)

AF:

0.849

AC:

9011

AN:

10612

Middle Eastern (MID)

AF:

0.769

AC:

226

AN:

294

European-Non Finnish (NFE)

AF:

0.776

AC:

52709

AN:

67958

Other (OTH)

AF:

0.768

AC:

1625

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1314

2628

3942

5256

6570

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.781

Hom.:

82547

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

(source)

DANN

Benign

0.69

PhyloP100

0.81

PromoterAI

0.15

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(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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10-59709780-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over