10-59689806-A-G

Variant names:

• chr10-59689806-A-G
• rs7094971
• NM_194298.3:c.-36-5479T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_194298.3(SLC16A9):​c.-36-5479T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,244 control chromosomes in the GnomAD database, including 1,373 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 0.13 (1373 hom., cov: 33)
• Consequence: SLC16A9 NM_194298.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37
• Publications: 34 publications found

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]

ACMG classification

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 = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_194298.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A9	NM_194298.3	MANE Select	c.-36-5479T>C		intron	N/A	NP_919274.1
	SLC16A9	NM_001323981.2		c.-36-5479T>C		intron	N/A	NP_001310910.1
	SLC16A9	NM_001323977.1		c.-167-5609T>C		intron	N/A	NP_001310906.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A9	ENST00000395348.8	TSL:5 MANE Select	c.-36-5479T>C		intron	N/A	ENSP00000378757.3
	SLC16A9	ENST00000395347.1	TSL:2	c.-36-5479T>C		intron	N/A	ENSP00000378756.1
	SLC16A9	ENST00000490066.1	TSL:5	n.223-5479T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19749 AN: 152126 Hom.: 1373 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.130 AC: 19754 AN: 152244 Hom.: 1373 Cov.: 33 AF XY: 0.126 AC XY: 9409 AN XY: 74462

African (AFR) AF: 0.138 AC: 5739 AN: 41548

American (AMR) AF: 0.114 AC: 1738 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5188

South Asian (SAS) AF: 0.113 AC: 544 AN: 4826

European-Finnish (FIN) AF: 0.0821 AC: 871 AN: 10604

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9714 AN: 67992

Other (OTH) AF: 0.146 AC: 309 AN: 2114

Alfa AF: 0.140 Hom.: 7099

Bravo AF: 0.134

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.3
DANN	Benign	0.84
PhyloP100		2.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7094971; hg19: chr10-61449564;