chr16-87832532-G-C

Variant names:

• chr16-87832532-G-C
• rs1060253
• NM_003486.7:c.*438C>G

Variant summary

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

The NM_003486.7(SLC7A5):​c.*438C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 153,570 control chromosomes in the GnomAD database, including 5,775 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 0.25 (5705 hom., cov: 31)
  • Exomes 𝑓: 0.26 (70 hom.)
• Consequence: SLC7A5 NM_003486.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

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 (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A5	NM_003486.7	c.*438C>G		3_prime_UTR_variant	Exon 10 of 10	ENST00000261622.5	NP_003477.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A5	ENST00000261622	c.*438C>G		3_prime_UTR_variant	Exon 10 of 10	1	NM_003486.7	ENSP00000261622.4
SLC7A5	ENST00000565644	c.*438C>G		3_prime_UTR_variant	Exon 10 of 10	1		ENSP00000454323.1
SLC7A5	ENST00000563489.1	n.*200C>G		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38492 AN: 151882 Hom.: 5703 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.259 AC: 407 AN: 1570 Hom.: 70 Cov.: 0 AF XY: 0.257 AC XY: 224 AN XY: 872

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.360

Gnomad4 ASJ exome AF: 0.100

Gnomad4 EAS exome AF: 0.615

Gnomad4 SAS exome AF: 0.218

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.237

Gnomad4 OTH exome AF: 0.274

GnomAD4 genome AF: 0.253 AC: 38501 AN: 152000 Hom.: 5705 Cov.: 31 AF XY: 0.257 AC XY: 19062 AN XY: 74296

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.250

Alfa AF: 0.272 Hom.: 864

Bravo AF: 0.259

Asia WGS AF: 0.380 AC: 1320 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	0.41
DANN	Benign	0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1060253; hg19: chr16-87866138;