chr16-87831663-C-CGGG

Position:

• chr16-87831663-C-CGGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_003486.7(SLC7A5):​c.*1306_*1307insCCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.53 (22958 hom., cov: 0)
  • Exomes 𝑓: 0.48 (6 hom.)
• Consequence: SLC7A5 NM_003486.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A5	NM_003486.7	c.*1306_*1307insCCC		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	ENST00000261622.5	c.*1306_*1307insCCC		3_prime_UTR_variant	10/10	1	NM_003486.7	ENSP00000261622	P1
SLC7A5	ENST00000565644.5	c.*1306_*1307insCCC		3_prime_UTR_variant	10/10	1		ENSP00000454323

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80479 AN: 151680 Hom.: 22915 Cov.: 0

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.495

GnomAD4 exome AF: 0.477 AC: 21 AN: 44 Hom.: 6 Cov.: 0 AF XY: 0.545 AC XY: 12 AN XY: 22

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.409

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.531 AC: 80576 AN: 151798 Hom.: 22958 Cov.: 0 AF XY: 0.538 AC XY: 39908 AN XY: 74190

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.493

Alfa AF: 0.265 Hom.: 459

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5818648; hg19: chr16-87865269;