Genetic Variant SLC16A9:c.1351+80T>C (chr10-59653595-A-G) – 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.1351+80T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,212,094 control chromosomes in the GnomAD database, including 14,147 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 0.12 ( 1321 hom., cov: 32)

Exomes 𝑓: 0.15 ( 12826 hom. )

Consequence

SLC16A9
NM_194298.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.453

Publications

56 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A9	NM_194298.3 link	c.1351+80T>C		intron_variant	Intron 5 of 5	ENST00000395348.8	NP_919274.1	Q7RTY1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A9	ENST00000395348.8 link	c.1351+80T>C		intron_variant	Intron 5 of 5	5	NM_194298.3	ENSP00000378757.3		Q7RTY1
SLC16A9	ENST00000395347.1 link	c.1351+80T>C		intron_variant	Intron 5 of 5	2		ENSP00000378756.1		Q7RTY1

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18367

AN:

152032

Hom.:

1323

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0736

Gnomad AMI

AF:

0.321

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0857

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.146

GnomAD4 exome

AF:

0.149

AC:

158291

AN:

1059942

Hom.:

12826

AF XY:

0.149

AC XY:

79451

AN XY:

534314

show subpopulations

African (AFR)

AF:

0.0715

AC:

1744

AN:

24394

American (AMR)

AF:

0.0917

AC:

2791

AN:

30452

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

3500

AN:

18698

East Asian (EAS)

AF:

0.000613

AC:

AN:

37498

South Asian (SAS)

AF:

0.125

AC:

8040

AN:

64078

European-Finnish (FIN)

AF:

0.0933

AC:

3545

AN:

38000

Middle Eastern (MID)

AF:

0.157

AC:

718

AN:

4586

European-Non Finnish (NFE)

AF:

0.165

AC:

131104

AN:

795504

Other (OTH)

AF:

0.146

AC:

6826

AN:

46732

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

6867

13734

20601

27468

34335

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4124

8248

12372

16496

20620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.121

AC:

18368

AN:

152152

Hom.:

1321

Cov.:

AF XY:

0.116

AC XY:

8656

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0735

AC:

3051

AN:

41508

American (AMR)

AF:

0.113

AC:

1726

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

601

AN:

3470

East Asian (EAS)

AF:

0.00116

AC:

AN:

5172

South Asian (SAS)

AF:

0.123

AC:

591

AN:

4816

European-Finnish (FIN)

AF:

0.0857

AC:

908

AN:

10590

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.160

AC:

10847

AN:

67990

Other (OTH)

AF:

0.146

AC:

308

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

794

1588

2381

3175

3969

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.151

Hom.:

8218

Bravo

AF:

0.121

Asia WGS

AF:

0.0580

AC:

202

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.5

(source)

DANN

Benign

0.82

PhyloP100

0.45

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over