16-87836773-A-G

Position:

• chr16-87836773-A-G

Variant summary

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

The NM_003486.7(SLC7A5):​c.1141-126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 890,950 control chromosomes in the GnomAD database, including 34,562 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 0.26 (5520 hom., cov: 32)
  • Exomes 𝑓: 0.28 (29042 hom.)
• Consequence: SLC7A5 NM_003486.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC7A5	NM_003486.7	c.1141-126T>C		intron_variant		ENST00000261622.5
LOC124903753	XR_007065175.1	n.509A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC7A5	ENST00000261622.5	c.1141-126T>C		intron_variant		1	NM_003486.7	P1
SLC7A5	ENST00000565644.5	c.343-126T>C		intron_variant		1
	ENST00000563687.1	n.242A>G		non_coding_transcript_exon_variant	1/2	3
SLC7A5	ENST00000563489.1	n.33T>C		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39820 AN: 151188 Hom.: 5502 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.0467

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.245

GnomAD4 exome AF: 0.284 AC: 210035 AN: 739640 Hom.: 29042 Cov.: 11 AF XY: 0.291 AC XY: 113094 AN XY: 389236

Gnomad4 AFR exome AF: 0.341

Gnomad4 AMR exome AF: 0.268

Gnomad4 ASJ exome AF: 0.297

Gnomad4 EAS exome AF: 0.0599

Gnomad4 SAS exome AF: 0.403

Gnomad4 FIN exome AF: 0.270

Gnomad4 NFE exome AF: 0.278

Gnomad4 OTH exome AF: 0.279

GnomAD4 genome AF: 0.264 AC: 39872 AN: 151310 Hom.: 5520 Cov.: 32 AF XY: 0.264 AC XY: 19502 AN XY: 73940

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.0468

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.242

Alfa AF: 0.259 Hom.: 5261

Bravo AF: 0.262

Asia WGS AF: 0.194 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.65

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: rs16943320; hg19: chr16-87870379;