NM_003486.7:c.*2307C>T

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

2

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

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
SLC7A5NM_003486.7 linkc.*2307C>T 3_prime_UTR_variant Exon 10 of 10 ENST00000261622.5 NP_003477.4 Q01650

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC7A5ENST00000261622.5 linkc.*2307C>T 3_prime_UTR_variant Exon 10 of 10 1 NM_003486.7 ENSP00000261622.4 Q01650
SLC7A5ENST00000565644.6 linkc.*2307C>T 3_prime_UTR_variant Exon 10 of 10 1 ENSP00000454323.1 A0A0C4DGL4
SLC7A5ENST00000850914.1 linkc.*2307C>T 3_prime_UTR_variant Exon 10 of 10 ENSP00000520997.1
ENSG00000260466ENST00000825115.1 linkn.248-6750G>A intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.0657
AC:
9994
AN:
152126
Hom.:
381
Cov.:
33
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:
9
AN:
142
Hom.:
1
Cov.:
0
AF XY:
0.0750
AC XY:
9
AN XY:
120
show subpopulations
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.482
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Hom
Variant carriers
0
2
4
6
8
10
<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.:
33
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:
43
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
0
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
0
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
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

Publications

Other links and lift over

dbSNP: rs16943300; hg19: chr16-87864269; API