rs16943300

Positions:

• chr16-87830663-G-A

Variant summary

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

The NM_003486.7(SLC7A5):​c.*2307C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 152,386 control chromosomes in the GnomAD database, including 382 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 0.066 (381 hom., cov: 33)
  • Exomes 𝑓: 0.063 (1 hom.)
• Consequence: SLC7A5 NM_003486.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A5	NM_003486.7	c.*2307C>T		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.*2307C>T		3_prime_UTR_variant	10/10	1	NM_003486.7	ENSP00000261622.4
SLC7A5	ENST00000565644.5	c.*2307C>T		3_prime_UTR_variant	10/10	1		ENSP00000454323.1

Frequencies

GnomAD3 genomes AF: 0.0657 AC: 9994 AN: 152126 Hom.: 381 Cov.: 33

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0393

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.0640

GnomAD4 exome AF: 0.0634 AC: 9 AN: 142 Hom.: 1 Cov.: 0 AF XY: 0.0750 AC XY: 9 AN XY: 120

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0455

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.0657 AC: 9997 AN: 152244 Hom.: 381 Cov.: 33 AF XY: 0.0664 AC XY: 4943 AN XY: 74420

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.0729

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0394

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0308

Gnomad4 NFE AF: 0.0627

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.0628 Hom.: 54

Bravo AF: 0.0659

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.3
DANN	Benign	0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

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: rs16943300; hg19: chr16-87864269;