10-59652577-A-G

Variant names:

• chr10-59652577-A-G
• rs3763747
• NM_194298.3:c.*195T>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.*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
• Publications: 8 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A9	NM_194298.3	MANE Select	c.*195T>C		3_prime_UTR	Exon 6 of 6	NP_919274.1	Q7RTY1
	SLC16A9	NM_001323981.2		c.*195T>C		3_prime_UTR	Exon 7 of 7	NP_001310910.1	Q7RTY1
	SLC16A9	NM_001323977.1		c.*195T>C		3_prime_UTR	Exon 6 of 6	NP_001310906.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A9	ENST00000395348.8	TSL:5 MANE Select	c.*195T>C		3_prime_UTR	Exon 6 of 6	ENSP00000378757.3	Q7RTY1
	SLC16A9	ENST00000881710.1		c.*195T>C		3_prime_UTR	Exon 6 of 6	ENSP00000551769.1
	SLC16A9	ENST00000881715.1		c.*195T>C		3_prime_UTR	Exon 7 of 7	ENSP00000551774.1

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

African (AFR) AF: 0.0552 AC: 433 AN: 7850

American (AMR) AF: 0.360 AC: 3406 AN: 9468

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 1399 AN: 10310

East Asian (EAS) AF: 0.569 AC: 12483 AN: 21940

South Asian (SAS) AF: 0.426 AC: 7681 AN: 18042

European-Finnish (FIN) AF: 0.345 AC: 7497 AN: 21748

Middle Eastern (MID) AF: 0.163 AC: 232 AN: 1424

European-Non Finnish (NFE) AF: 0.224 AC: 44420 AN: 198406

Other (OTH) AF: 0.239 AC: 4476 AN: 18696

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

African (AFR) AF: 0.0570 AC: 2367 AN: 41552

American (AMR) AF: 0.308 AC: 4688 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 501 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3013 AN: 5154

South Asian (SAS) AF: 0.457 AC: 2195 AN: 4808

European-Finnish (FIN) AF: 0.342 AC: 3590 AN: 10494

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15996 AN: 67926

Other (OTH) AF: 0.215 AC: 454 AN: 2108

Alfa AF: 0.229 Hom.: 4709

Bravo AF: 0.205

Asia WGS AF: 0.480 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.86
DANN	Benign	0.54
PhyloP100		0.11
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: rs3763747; hg19: chr10-61412335;