16-87838108-T-G

Position:

• chr16-87838108-T-G

Variant summary

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

The NM_003486.7(SLC7A5):​c.1044-167A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,024 control chromosomes in the GnomAD database, including 34,756 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 0.67 (34756 hom., cov: 33)
• Consequence: SLC7A5 NM_003486.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC7A5	NM_003486.7	c.1044-167A>C		intron_variant		ENST00000261622.5	NP_003477.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC7A5	ENST00000261622.5	c.1044-167A>C		intron_variant		1	NM_003486.7	ENSP00000261622.4
SLC7A5	ENST00000565644.5	c.246-167A>C		intron_variant		1		ENSP00000454323.1

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101451 AN: 151906 Hom.: 34704 Cov.: 33

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.627

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.668 AC: 101556 AN: 152024 Hom.: 34756 Cov.: 33 AF XY: 0.678 AC XY: 50395 AN XY: 74320

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.625

Alfa AF: 0.586 Hom.: 24947

Bravo AF: 0.674

Asia WGS AF: 0.824 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.47
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: rs2287121; hg19: chr16-87871714;