16-87831688-C-T

Position:

• chr16-87831688-C-T

Variant summary

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

The NM_003486.7(SLC7A5):​c.*1282G>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 0.317 in 152,138 control chromosomes in the GnomAD database, including 8,061 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 0.32 (8056 hom., cov: 33)
  • Exomes 𝑓: 0.47 (5 hom.)
• Consequence: SLC7A5 NM_003486.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

SLC7A5 (HGNC:11063): (solute carrier family 7 member 5) Enables L-leucine transmembrane transporter activity; L-tryptophan transmembrane transporter activity; and thyroid hormone transmembrane transporter activity. Involved in carboxylic acid transport; thyroid hormone transport; and xenobiotic transport. Located in cytosol; intracellular membrane-bounded organelle; and plasma membrane. Is integral component of membrane. Part of amino acid transport complex; apical plasma membrane; and microvillus 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A5	NM_003486.7	c.*1282G>A		3_prime_UTR_variant	10/10	ENST00000261622.5	NP_003477.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A5	ENST00000261622	c.*1282G>A		3_prime_UTR_variant	10/10	1	NM_003486.7	ENSP00000261622.4
SLC7A5	ENST00000565644	c.*1282G>A		3_prime_UTR_variant	10/10	1		ENSP00000454323.1

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48140 AN: 151982 Hom.: 8046 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.474 AC: 18 AN: 38 Hom.: 5 Cov.: 0 AF XY: 0.409 AC XY: 9 AN XY: 22

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.409

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.317 AC: 48177 AN: 152100 Hom.: 8056 Cov.: 33 AF XY: 0.320 AC XY: 23757 AN XY: 74352

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.295

Alfa AF: 0.303 Hom.: 1097

Bravo AF: 0.330

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.6
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1060257; hg19: chr16-87865294; COSMIC: COSV55366178; COSMIC: COSV55366178;