10-59654442-T-C

Variant names:

• chr10-59654442-T-C
• NM_194298.3:c.584A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_194298.3(SLC16A9):​c.584A>G​(p.Asp195Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC16A9 NM_194298.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.161
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.034683615).

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.584A>G	p.Asp195Gly	missense	Exon 5 of 6	NP_919274.1	Q7RTY1
	SLC16A9	NM_001323981.2		c.584A>G	p.Asp195Gly	missense	Exon 6 of 7	NP_001310910.1	Q7RTY1
	SLC16A9	NM_001323977.1		c.323A>G	p.Asp108Gly	missense	Exon 5 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.584A>G	p.Asp195Gly	missense	Exon 5 of 6	ENSP00000378757.3	Q7RTY1
	SLC16A9	ENST00000881710.1		c.584A>G	p.Asp195Gly	missense	Exon 5 of 6	ENSP00000551769.1
	SLC16A9	ENST00000881715.1		c.584A>G	p.Asp195Gly	missense	Exon 6 of 7	ENSP00000551774.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.070
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	7.0
DANN	Benign	0.79
DEOGEN2	Benign	0.050	T
Eigen	Benign	-1.0
Eigen_PC	Benign	-0.99
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.62	T
M_CAP	Benign	0.015	T
MetaRNN	Benign	0.035	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-0.39	N
PhyloP100		0.16
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-0.62	N
REVEL	Benign	0.15
Sift	Benign	0.44	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.11
MutPred		0.50		Gain of glycosylation at S194 (P = 0.0246)
MVP		0.15
MPC		0.16
ClinPred		0.025	T
GERP RS		-0.25
Varity_R		0.079
gMVP		0.40
Mutation Taster		=84/16	polymorphism

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

hg19: chr10-61414200;