chr10-59652577-A-C

Variant names:

• chr10-59652577-A-C
• rs3763747
• NM_194298.3:c.*195T>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.*195T>G variant causes a 3 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• 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: 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 (BayesDel_noAF=-0.84).

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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A9	ENST00000395348.8	TSL:5 MANE Select	c.*195T>G		3_prime_UTR	Exon 6 of 6	ENSP00000378757.3
	SLC16A9	ENST00000395347.1	TSL:2	c.*195T>G		3_prime_UTR	Exon 6 of 6	ENSP00000378756.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 4

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 4709

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.87
DANN	Benign	0.52
PhyloP100		0.11

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;