rs7094971

chr10-59689806-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A9	NM_194298.3	c.-36-5479T>C		intron_variant		ENST00000395348.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A9	ENST00000395348.8	c.-36-5479T>C		intron_variant		5	NM_194298.3	P1
SLC16A9	ENST00000395347.1	c.-36-5479T>C		intron_variant		2		P1
SLC16A9	ENST00000490066.1	n.223-5479T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0821

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.146

Alfa AF: 0.142 Hom.: 3510

Bravo AF: 0.134

Asia WGS AF: 0.0580 AC: 203 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	9.3
Dann	Benign	0.84

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

Other links and lift over

dbSNP: rs7094971; hg19: chr10-61449564;