10-59652577-A-G

Position:

• chr10-59652577-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.*195T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 459,840 control chromosomes in the GnomAD database, including 18,144 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 0.22 (4968 hom., cov: 31)
  • Exomes 𝑓: 0.27 (13176 hom.)
• Consequence: SLC16A9 NM_194298.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A9	NM_194298.3	c.*195T>C		3_prime_UTR_variant	6/6	ENST00000395348.8	NP_919274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC16A9	ENST00000395348	c.*195T>C		3_prime_UTR_variant	6/6	5	NM_194298.3	ENSP00000378757.3
SLC16A9	ENST00000395347	c.*195T>C		3_prime_UTR_variant	6/6	2		ENSP00000378756.1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32953 AN: 151838 Hom.: 4955 Cov.: 31

Gnomad AFR AF: 0.0571

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.209

GnomAD4 exome AF: 0.266 AC: 82027 AN: 307884 Hom.: 13176 Cov.: 4 AF XY: 0.271 AC XY: 43306 AN XY: 159814

Gnomad4 AFR exome AF: 0.0552

Gnomad4 AMR exome AF: 0.360

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.569

Gnomad4 SAS exome AF: 0.426

Gnomad4 FIN exome AF: 0.345

Gnomad4 NFE exome AF: 0.224

Gnomad4 OTH exome AF: 0.239

GnomAD4 genome AF: 0.217 AC: 32982 AN: 151956 Hom.: 4968 Cov.: 31 AF XY: 0.227 AC XY: 16886 AN XY: 74238

Gnomad4 AFR AF: 0.0570

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.215

Alfa AF: 0.231 Hom.: 3550

Bravo AF: 0.205

Asia WGS AF: 0.480 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.86
DANN	Benign	0.54

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: rs3763747; hg19: chr10-61412335;