Genetic Variant NM_003486.7:c.*2307C>T (chr16-87830663-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.811

Publications

5 publications found

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 Gene-Disease associations (from GenCC):

complex neurodevelopmental disorder
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

SLC7A5 links:

ENSG00000260466 (HGNC:58301):

ENSG00000260466 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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 link	c.*2307C>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000261622.5	NP_003477.4	Q01650

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC7A5	ENST00000261622.5 link	c.*2307C>T	3_prime_UTR_variant	Exon 10 of 10	1	NM_003486.7	ENSP00000261622.4	Q01650
SLC7A5	ENST00000565644.6 link	c.*2307C>T	3_prime_UTR_variant	Exon 10 of 10	1		ENSP00000454323.1	A0A0C4DGL4
SLC7A5	ENST00000850914.1 link	c.*2307C>T	3_prime_UTR_variant	Exon 10 of 10			ENSP00000520997.1
ENSG00000260466	ENST00000825115.1 link	n.248-6750G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0657

AC:

9994

AN:

152126

Hom.:

381

Cov.:

show subpopulations

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:

AN:

142

Hom.:

Cov.:

AF XY:

0.0750

AC XY:

AN XY:

120

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.333

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0455

AC:

AN:

110

Other (OTH)

AF:

0.0833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0657

AC:

9997

AN:

152244

Hom.:

381

Cov.:

AF XY:

0.0664

AC XY:

4943

AN XY:

74420

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0627

AC:

4266

AN:

68004

Other (OTH)

AF:

0.0638

AC:

135

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

479

958

1438

1917

2396

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over