NM_003486.7:c.*2307C>T

Variant names:

• chr16-87830663-G-A
• rs16943300
• NM_003486.7:c.*2307C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

SLC7A5 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000260466 (HGNC:58301):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC7A5	NM_003486.7	c.*2307C>T		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	ENST00000261622.5	c.*2307C>T		3_prime_UTR_variant	Exon 10 of 10	1	NM_003486.7	ENSP00000261622.4
SLC7A5	ENST00000565644.6	c.*2307C>T		3_prime_UTR_variant	Exon 10 of 10	1		ENSP00000454323.1
SLC7A5	ENST00000850914.1	c.*2307C>T		3_prime_UTR_variant	Exon 10 of 10			ENSP00000520997.1
ENSG00000260466	ENST00000825115.1	n.248-6750G>A		intron_variant	Intron 1 of 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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.333 AC: 2 AN: 6

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.0455 AC: 5 AN: 110

Other (OTH) AF: 0.0833 AC: 1 AN: 12

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

African (AFR) AF: 0.0608 AC: 2524 AN: 41542

American (AMR) AF: 0.0729 AC: 1115 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.0394 AC: 204 AN: 5174

South Asian (SAS) AF: 0.148 AC: 716 AN: 4828

European-Finnish (FIN) AF: 0.0308 AC: 327 AN: 10612

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0627 AC: 4266 AN: 68004

Other (OTH) AF: 0.0638 AC: 135 AN: 2116

Alfa AF: 0.0645 Hom.: 523

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
PhyloP100		-0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16943300; hg19: chr16-87864269;