10-59653595-A-G

Variant names:

• chr10-59653595-A-G
• rs12356193
• NM_194298.3:c.1351+80T>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.1351+80T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 1,212,094 control chromosomes in the GnomAD database, including 14,147 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 0.12 (1321 hom., cov: 32)
  • Exomes 𝑓: 0.15 (12826 hom.)
• Consequence: SLC16A9 NM_194298.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 56 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 = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A9	NM_194298.3	c.1351+80T>C		intron_variant	Intron 5 of 5	ENST00000395348.8	NP_919274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A9	ENST00000395348.8	c.1351+80T>C		intron_variant	Intron 5 of 5	5	NM_194298.3	ENSP00000378757.3
SLC16A9	ENST00000395347.1	c.1351+80T>C		intron_variant	Intron 5 of 5	2		ENSP00000378756.1

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18367 AN: 152032 Hom.: 1323 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0857

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.146

GnomAD4 exome AF: 0.149 AC: 158291 AN: 1059942 Hom.: 12826 AF XY: 0.149 AC XY: 79451 AN XY: 534314

African (AFR) AF: 0.0715 AC: 1744 AN: 24394

American (AMR) AF: 0.0917 AC: 2791 AN: 30452

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 3500 AN: 18698

East Asian (EAS) AF: 0.000613 AC: 23 AN: 37498

South Asian (SAS) AF: 0.125 AC: 8040 AN: 64078

European-Finnish (FIN) AF: 0.0933 AC: 3545 AN: 38000

Middle Eastern (MID) AF: 0.157 AC: 718 AN: 4586

European-Non Finnish (NFE) AF: 0.165 AC: 131104 AN: 795504

Other (OTH) AF: 0.146 AC: 6826 AN: 46732

GnomAD4 genome AF: 0.121 AC: 18368 AN: 152152 Hom.: 1321 Cov.: 32 AF XY: 0.116 AC XY: 8656 AN XY: 74388

African (AFR) AF: 0.0735 AC: 3051 AN: 41508

American (AMR) AF: 0.113 AC: 1726 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5172

South Asian (SAS) AF: 0.123 AC: 591 AN: 4816

European-Finnish (FIN) AF: 0.0857 AC: 908 AN: 10590

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10847 AN: 67990

Other (OTH) AF: 0.146 AC: 308 AN: 2116

Alfa AF: 0.151 Hom.: 8218

Bravo AF: 0.121

Asia WGS AF: 0.0580 AC: 202 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	6.5
DANN	Benign	0.82
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs12356193; hg19: chr10-61413353;