Variant 10-59652801-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_194298.3(SLC16A9):c.1501T>G(p.Phe501Val) variant causes a missense change. The variant allele was found at a frequency of 0.0131 in 1,611,346 control chromosomes in the GnomAD database, including 185 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0078 ( 6 hom., cov: 32)

Exomes 𝑓: 0.014 ( 179 hom. )

Consequence

SLC16A9
NM_194298.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.03

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.003896594).

BP6

Variant 10-59652801-A-C is Benign according to our data. Variant chr10-59652801-A-C is described in ClinVar as [Benign]. Clinvar id is 774470.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0137 (19946/1459096) while in subpopulation NFE AF= 0.0167 (18595/1111234). AF 95% confidence interval is 0.0165. There are 179 homozygotes in gnomad4_exome. There are 9586 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A9	NM_194298.3 linkuse as main transcript	c.1501T>G	p.Phe501Val	missense_variant	6/6	ENST00000395348.8	NP_919274.1	Q7RTY1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A9	ENST00000395348.8 linkuse as main transcript	c.1501T>G	p.Phe501Val	missense_variant	6/6	5	NM_194298.3	ENSP00000378757.3		Q7RTY1
SLC16A9	ENST00000395347.1 linkuse as main transcript	c.1501T>G	p.Phe501Val	missense_variant	6/6	2		ENSP00000378756.1		Q7RTY1

Frequencies

GnomAD3 genomes

AF:

0.00786

AC:

1195

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00237

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00413

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00650

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0139

Gnomad OTH

AF:

0.00383

GnomAD3 exomes

AF:

0.00780

AC:

1935

AN:

248186

Hom.:

AF XY:

0.00799

AC XY:

1070

AN XY:

134000

show subpopulations

Gnomad AFR exome

AF:

0.00240

Gnomad AMR exome

AF:

0.00260

Gnomad ASJ exome

AF:

0.00332

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000678

Gnomad FIN exome

AF:

0.00824

Gnomad NFE exome

AF:

0.0138

Gnomad OTH exome

AF:

0.00708

GnomAD4 exome

AF:

0.0137

AC:

19946

AN:

1459096

Hom.:

179

Cov.:

AF XY:

0.0132

AC XY:

9586

AN XY:

725704

show subpopulations

Gnomad4 AFR exome

AF:

0.00192

Gnomad4 AMR exome

AF:

0.00302

Gnomad4 ASJ exome

AF:

0.00253

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000199

Gnomad4 FIN exome

AF:

0.00719

Gnomad4 NFE exome

AF:

0.0167

Gnomad4 OTH exome

AF:

0.0114

GnomAD4 genome

AF:

0.00785

AC:

1195

AN:

152250

Hom.:

Cov.:

AF XY:

0.00720

AC XY:

536

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.00236

Gnomad4 AMR

AF:

0.00412

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00650

Gnomad4 NFE

AF:

0.0139

Gnomad4 OTH

AF:

0.00379

Alfa

AF:

0.0125

Hom.:

Bravo

AF:

0.00781

TwinsUK

AF:

0.0178

AC:

ALSPAC

AF:

0.0145

AC:

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.0137

AC:

118

ExAC

AF:

0.00736

AC:

893

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.0141

EpiControl

AF:

0.0122

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 13, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0050

T;T

Eigen

Benign

-0.28

Eigen_PC

Benign

-0.12

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.77

.;T

MetaRNN

Benign

0.0039

T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.69

N;N

PrimateAI

Benign

0.43

PROVEAN

Benign

-0.050

N;N

REVEL

Benign

0.11

Sift

Benign

0.16

T;T

Sift4G

Uncertain

0.016

D;D

Polyphen

0.081

B;B

Vest4

0.15

MVP

0.043

MPC

0.20

ClinPred

0.016

GERP RS

5.6

Varity_R

0.10

gMVP

0.52

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over