rs14399

chr6-111222741-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018593.5(SLC16A10):c.*506C>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 0.333 in 154,528 control chromosomes in the GnomAD database, including 10,337 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 0.33 (10163 hom., cov: 32)
  • Exomes 𝑓: 0.36 (174 hom.)
• Consequence: SLC16A10 NM_018593.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

Genes affected

SLC16A10 (HGNC:17027): (solute carrier family 16 member 10) SLC16A10 is a member of a family of plasma membrane amino acid transporters that mediate the Na(+)-independent transport of aromatic amino acids across the plasma membrane.[supplied by OMIM, Apr 2004]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A10	NM_018593.5	c.*506C>A		3_prime_UTR_variant	6/6	ENST00000368851.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A10	ENST00000368851.10	c.*506C>A		3_prime_UTR_variant	6/6	1	NM_018593.5	P1
SLC16A10	ENST00000368850.4	c.*506C>A		3_prime_UTR_variant	5/5	1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50599 AN: 151928 Hom.: 10161 Cov.: 32

Gnomad AFR AF: 0.0963

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.369

GnomAD4 exome AF: 0.359 AC: 891 AN: 2480 Hom.: 174 Cov.: 0 AF XY: 0.366 AC XY: 552 AN XY: 1510

Gnomad4 AFR exome AF: 0.0357

Gnomad4 AMR exome AF: 0.313

Gnomad4 ASJ exome AF: 0.455

Gnomad4 EAS exome AF: 0.515

Gnomad4 SAS exome AF: 0.439

Gnomad4 FIN exome AF: 0.297

Gnomad4 NFE exome AF: 0.357

Gnomad4 OTH exome AF: 0.351

GnomAD4 genome AF: 0.333 AC: 50618 AN: 152048 Hom.: 10163 Cov.: 32 AF XY: 0.336 AC XY: 24983 AN XY: 74326

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.366

Alfa AF: 0.356 Hom.: 2762

Bravo AF: 0.324

Asia WGS AF: 0.482 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	6.7
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: rs14399; hg19: chr6-111543944; COSMIC: COSV64353938;