NM_003486.7:c.*438C>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 28 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 (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003486.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC7A5	NM_003486.7	MANE Select	c.*438C>G		3_prime_UTR	Exon 10 of 10	NP_003477.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC7A5	ENST00000261622.5	TSL:1 MANE Select	c.*438C>G		3_prime_UTR	Exon 10 of 10	ENSP00000261622.4
	SLC7A5	ENST00000565644.6	TSL:1	c.*438C>G		3_prime_UTR	Exon 10 of 10	ENSP00000454323.1
	SLC7A5	ENST00000850914.1		c.*438C>G		3_prime_UTR	Exon 10 of 10	ENSP00000520997.1

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

African (AFR) AF: 0.167 AC: 2 AN: 12

American (AMR) AF: 0.360 AC: 82 AN: 228

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 1 AN: 10

East Asian (EAS) AF: 0.615 AC: 16 AN: 26

South Asian (SAS) AF: 0.218 AC: 24 AN: 110

European-Finnish (FIN) AF: 0.167 AC: 2 AN: 12

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.237 AC: 263 AN: 1108

Other (OTH) AF: 0.274 AC: 17 AN: 62

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

African (AFR) AF: 0.133 AC: 5524 AN: 41492

American (AMR) AF: 0.377 AC: 5759 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3472

East Asian (EAS) AF: 0.592 AC: 3045 AN: 5146

South Asian (SAS) AF: 0.196 AC: 946 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2912 AN: 10568

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18803 AN: 67898

Other (OTH) AF: 0.250 AC: 528 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.41
DANN	Benign	0.51
PhyloP100		-1.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs1060253; hg19: chr16-87866138;