Genetic Variant NM_003486.7:c.1141-126T>C (chr16-87836773-A-G) – 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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.549

Publications

10 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=-0.85).

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 rank	MANE	Protein	UniProt
SLC7A5	NM_003486.7 link	c.1141-126T>C		intron_variant	Intron 7 of 9	ENST00000261622.5	NP_003477.4	Q01650
SLC7A5-AS1	XR_007065175.1 link	n.509A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A5	ENST00000261622.5 link	c.1141-126T>C		intron_variant	Intron 7 of 9	1	NM_003486.7	ENSP00000261622.4		Q01650

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39820

AN:

151188

Hom.:

5502

Cov.:

show subpopulations

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.:

AF XY:

0.291

AC XY:

113094

AN XY:

389236

show subpopulations

African (AFR)

AF:

0.341

AC:

6487

AN:

19022

American (AMR)

AF:

0.268

AC:

9462

AN:

35288

Ashkenazi Jewish (ASJ)

AF:

0.297

AC:

5741

AN:

19334

East Asian (EAS)

AF:

0.0599

AC:

1626

AN:

27144

South Asian (SAS)

AF:

0.403

AC:

28141

AN:

69776

European-Finnish (FIN)

AF:

0.270

AC:

8227

AN:

30452

Middle Eastern (MID)

AF:

0.361

AC:

1406

AN:

3890

European-Non Finnish (NFE)

AF:

0.278

AC:

139308

AN:

500240

Other (OTH)

AF:

0.279

AC:

9637

AN:

34494

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

8474

16949

25423

33898

42372

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3080

6160

9240

12320

15400

<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:

0.264

AC:

39872

AN:

151310

Hom.:

5520

Cov.:

AF XY:

0.264

AC XY:

19502

AN XY:

73940

show subpopulations

African (AFR)

AF:

0.305

AC:

12580

AN:

41264

American (AMR)

AF:

0.249

AC:

3800

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.242

AC:

837

AN:

3454

East Asian (EAS)

AF:

0.0468

AC:

237

AN:

5064

South Asian (SAS)

AF:

0.384

AC:

1840

AN:

4786

European-Finnish (FIN)

AF:

0.237

AC:

2467

AN:

10406

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.252

AC:

17072

AN:

67802

Other (OTH)

AF:

0.242

AC:

508

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1455

2910

4366

5821

7276

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.260

Hom.:

6913

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

(source)

DANN

Benign

0.65

PhyloP100

-0.55

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