chr10-59651934-C-T

Position:

• chr10-59651934-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_194298.3(SLC16A9):​c.*838G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0297 in 152,216 control chromosomes in the GnomAD database, including 103 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 0.030 (103 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC16A9 NM_194298.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38

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=-0.66).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0297 (4520/152216) while in subpopulation NFE AF= 0.0451 (3066/68014). AF 95% confidence interval is 0.0437. There are 103 homozygotes in gnomad4. There are 2171 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 103 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC16A9	NM_194298.3	c.*838G>A		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.*838G>A		3_prime_UTR_variant	6/6	5	NM_194298.3	ENSP00000378757.3
SLC16A9	ENST00000395347	c.*838G>A		3_prime_UTR_variant	6/6	2		ENSP00000378756.1

Frequencies

GnomAD3 genomes AF: 0.0297 AC: 4520 AN: 152098 Hom.: 103 Cov.: 33

Gnomad AFR AF: 0.00739

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0451

Gnomad OTH AF: 0.0297

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0297 AC: 4520 AN: 152216 Hom.: 103 Cov.: 33 AF XY: 0.0292 AC XY: 2171 AN XY: 74418

Gnomad4 AFR AF: 0.00737

Gnomad4 AMR AF: 0.0264

Gnomad4 ASJ AF: 0.0727

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0451

Gnomad4 OTH AF: 0.0294

Alfa AF: 0.0437 Hom.: 167

Bravo AF: 0.0291

Asia WGS AF: 0.00866 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.019
DANN	Benign	0.73

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: rs2893808; hg19: chr10-61411692;