rs14399

Variant names:

• chr6-111222741-C-A
• rs14399
• NM_018593.5:c.*506C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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]

MFSD4B-DT (HGNC:55773): (MFSD4B divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC16A10	NM_018593.5	c.*506C>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000368851.10	NP_061063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A10	ENST00000368851.10	c.*506C>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_018593.5	ENSP00000357844.4

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

African (AFR) AF: 0.0357 AC: 1 AN: 28

American (AMR) AF: 0.313 AC: 5 AN: 16

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 10 AN: 22

East Asian (EAS) AF: 0.515 AC: 35 AN: 68

South Asian (SAS) AF: 0.439 AC: 43 AN: 98

European-Finnish (FIN) AF: 0.297 AC: 22 AN: 74

Middle Eastern (MID) AF: 0.375 AC: 3 AN: 8

European-Non Finnish (NFE) AF: 0.357 AC: 725 AN: 2032

Other (OTH) AF: 0.351 AC: 47 AN: 134

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

African (AFR) AF: 0.0961 AC: 3988 AN: 41508

American (AMR) AF: 0.410 AC: 6262 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1456 AN: 3466

East Asian (EAS) AF: 0.532 AC: 2746 AN: 5166

South Asian (SAS) AF: 0.508 AC: 2450 AN: 4822

European-Finnish (FIN) AF: 0.363 AC: 3824 AN: 10532

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28693 AN: 67964

Other (OTH) AF: 0.366 AC: 771 AN: 2108

Alfa AF: 0.350 Hom.: 2767

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
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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: rs14399; hg19: chr6-111543944; COSMIC: COSV64353938;