Genetic Variant SLC7A5:c.1141-59G>A (chr16-87836706-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003486.7(SLC7A5):c.1141-59G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 1,590,380 control chromosomes in the GnomAD database, including 51,572 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 ( 5521 hom., cov: 33)

Exomes 𝑓: 0.25 ( 46051 hom. )

Consequence

SLC7A5
NM_003486.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.291

Variant links:

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 links:

ENSG00000260466 (HGNC:58301):

ENSG00000260466 links:

LOC124903753 (HGNC:):

LOC124903753 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A5	NM_003486.7 link	c.1141-59G>A		intron_variant	Intron 7 of 9	ENST00000261622.5	NP_003477.4	Q01650
LOC124903753	XR_007065175.1 link	n.442C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC7A5	ENST00000261622.5 link	c.1141-59G>A	intron_variant	Intron 7 of 9	1	NM_003486.7	ENSP00000261622.4	Q01650
SLC7A5	ENST00000565644.5 link	c.343-59G>A	intron_variant	Intron 7 of 9	1		ENSP00000454323.1	A0A0C4DGL4
SLC7A5	ENST00000563489.1 link	n.100G>A	non_coding_transcript_exon_variant	Exon 1 of 3	2
ENSG00000260466	ENST00000563687.1 link	n.175C>T	non_coding_transcript_exon_variant	Exon 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39824

AN:

152044

Hom.:

5504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.469

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.242

Gnomad EAS

AF:

0.0416

Gnomad SAS

AF:

0.384

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.328

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.244

GnomAD4 exome

AF:

0.246

AC:

353237

AN:

1438218

Hom.:

46051

Cov.:

AF XY:

0.251

AC XY:

180065

AN XY:

716452

show subpopulations

Gnomad4 AFR exome

AF:

0.309

Gnomad4 AMR exome

AF:

0.255

Gnomad4 ASJ exome

AF:

0.266

Gnomad4 EAS exome

AF:

0.0449

Gnomad4 SAS exome

AF:

0.396

Gnomad4 FIN exome

AF:

0.236

Gnomad4 NFE exome

AF:

0.239

Gnomad4 OTH exome

AF:

0.239

GnomAD4 genome

AF:

0.262

AC:

39875

AN:

152162

Hom.:

5521

Cov.:

AF XY:

0.262

AC XY:

19506

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.249

Gnomad4 ASJ

AF:

0.242

Gnomad4 EAS

AF:

0.0417

Gnomad4 SAS

AF:

0.383

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.251

Gnomad4 OTH

AF:

0.241

Alfa

AF:

0.276

Hom.:

748

Bravo

AF:

0.261

Asia WGS

AF:

0.193

AC:

673

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.19

DANN

Benign

0.60

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over