dbSNP rs41318021: SLC7A1:c.*10C>T (chr13-29514470-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_003045.5(SLC7A1):c.*10C>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 0.0843 in 1,601,734 control chromosomes in the GnomAD database, including 6,737 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 0.063 ( 457 hom., cov: 33)

Exomes 𝑓: 0.087 ( 6280 hom. )

Consequence

SLC7A1
NM_003045.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.213

Publications

13 publications found

Variant links:

Genes affected

SLC7A1 (HGNC:11057): (solute carrier family 7 member 1) Enables L-arginine transmembrane transporter activity and L-histidine transmembrane transporter activity. Involved in amino acid transport. Located in membrane. Part of apical plasma membrane; basolateral plasma membrane; and protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

SLC7A1 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=-0.55).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC7A1	NM_003045.5 link	c.*10C>T		3_prime_UTR_variant	Exon 13 of 13	ENST00000380752.10	NP_003036.1	P30825A0A024RDQ9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC7A1	ENST00000380752.10 link	c.*10C>T		3_prime_UTR_variant	Exon 13 of 13	1	NM_003045.5	ENSP00000370128.5		P30825

Frequencies

GnomAD3 genomes

AF:

0.0634

AC:

9642

AN:

152168

Hom.:

457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0155

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.0438

Gnomad ASJ

AF:

0.0334

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0317

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0949

Gnomad OTH

AF:

0.0455

GnomAD2 exomes

AF:

0.0661

AC:

16028

AN:

242302

AF XY:

0.0672

show subpopulations

Gnomad AFR exome

AF:

0.0134

Gnomad AMR exome

AF:

0.0342

Gnomad ASJ exome

AF:

0.0330

Gnomad EAS exome

AF:

0.000220

Gnomad FIN exome

AF:

0.143

Gnomad NFE exome

AF:

0.0949

Gnomad OTH exome

AF:

0.0643

GnomAD4 exome

AF:

0.0866

AC:

125456

AN:

1449448

Hom.:

6280

Cov.:

AF XY:

0.0848

AC XY:

61184

AN XY:

721530

show subpopulations

African (AFR)

AF:

0.0116

AC:

388

AN:

33406

American (AMR)

AF:

0.0336

AC:

1499

AN:

44660

Ashkenazi Jewish (ASJ)

AF:

0.0342

AC:

892

AN:

26058

East Asian (EAS)

AF:

0.000202

AC:

AN:

39676

South Asian (SAS)

AF:

0.0353

AC:

3038

AN:

86094

European-Finnish (FIN)

AF:

0.139

AC:

6424

AN:

46244

Middle Eastern (MID)

AF:

0.0192

AC:

109

AN:

5680

European-Non Finnish (NFE)

AF:

0.0982

AC:

108751

AN:

1107526

Other (OTH)

AF:

0.0723

AC:

4347

AN:

60104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

5677

11354

17032

22709

28386

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3840

7680

11520

15360

19200

<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:

0.0633

AC:

9644

AN:

152286

Hom.:

457

Cov.:

AF XY:

0.0632

AC XY:

4702

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.0155

AC:

644

AN:

41580

American (AMR)

AF:

0.0439

AC:

672

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0334

AC:

116

AN:

3468

East Asian (EAS)

AF:

0.00116

AC:

AN:

5178

South Asian (SAS)

AF:

0.0321

AC:

155

AN:

4822

European-Finnish (FIN)

AF:

0.134

AC:

1421

AN:

10618

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0948

AC:

6449

AN:

67998

Other (OTH)

AF:

0.0445

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

447

893

1340

1786

2233

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0660

Hom.:

210

Bravo

AF:

0.0540

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

5.9

(source)

DANN

Benign

0.86

PhyloP100

0.21

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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