dbSNP rs2070246: SLC1A5:p.Tyr276Tyr (chr19-46778905-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005628.3(SLC1A5):c.828C>T(p.Tyr276Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 1,557,940 control chromosomes in the GnomAD database, including 45,213 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 0.29 ( 7320 hom., cov: 32)

Exomes 𝑓: 0.22 ( 37893 hom. )

Consequence

SLC1A5
NM_005628.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.546

Publications

24 publications found

Variant links:

Genes affected

SLC1A5 (HGNC:10943): (solute carrier family 1 member 5) The SLC1A5 gene encodes a sodium-dependent neutral amino acid transporter that can act as a receptor for RD114/type D retrovirus (Larriba et al., 2001 [PubMed 11781704]).[supplied by OMIM, Jan 2011]

SLC1A5 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP7

Synonymous conserved (PhyloP=-0.546 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC1A5	NM_005628.3 link	c.828C>T	p.Tyr276Tyr	synonymous_variant	Exon 5 of 8	ENST00000542575.6	NP_005619.1	Q15758-1Q59ES3
SLC1A5	NM_001145145.2 link	c.222C>T	p.Tyr74Tyr	synonymous_variant	Exon 4 of 7		NP_001138617.1	Q15758-2
SLC1A5	NM_001145144.2 link	c.144C>T	p.Tyr48Tyr	synonymous_variant	Exon 5 of 8		NP_001138616.1	Q15758-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC1A5	ENST00000542575.6 link	c.828C>T	p.Tyr276Tyr	synonymous_variant	Exon 5 of 8	1	NM_005628.3	ENSP00000444408.1		Q15758-1

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

44086

AN:

152046

Hom.:

7303

Cov.:

show subpopulations

Gnomad AFR

AF:

0.436

Gnomad AMI

AF:

0.225

Gnomad AMR

AF:

0.383

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.287

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.281

GnomAD2 exomes

AF:

0.271

AC:

55351

AN:

203922

AF XY:

0.261

show subpopulations

Gnomad AFR exome

AF:

0.440

Gnomad AMR exome

AF:

0.443

Gnomad ASJ exome

AF:

0.229

Gnomad EAS exome

AF:

0.259

Gnomad FIN exome

AF:

0.196

Gnomad NFE exome

AF:

0.205

Gnomad OTH exome

AF:

0.263

GnomAD4 exome

AF:

0.224

AC:

314753

AN:

1405774

Hom.:

37893

Cov.:

AF XY:

0.225

AC XY:

155822

AN XY:

693240

show subpopulations

African (AFR)

AF:

0.445

AC:

14300

AN:

32142

American (AMR)

AF:

0.434

AC:

16704

AN:

38490

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

4659

AN:

21930

East Asian (EAS)

AF:

0.289

AC:

11355

AN:

39342

South Asian (SAS)

AF:

0.281

AC:

21371

AN:

76082

European-Finnish (FIN)

AF:

0.192

AC:

9786

AN:

50890

Middle Eastern (MID)

AF:

0.250

AC:

1371

AN:

5478

European-Non Finnish (NFE)

AF:

0.205

AC:

221636

AN:

1083428

Other (OTH)

AF:

0.234

AC:

13571

AN:

57992

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

11741

23482

35224

46965

58706

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8212

16424

24636

32848

41060

<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:

0.290

AC:

44153

AN:

152166

Hom.:

7320

Cov.:

AF XY:

0.293

AC XY:

21776

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.436

AC:

18103

AN:

41500

American (AMR)

AF:

0.382

AC:

5845

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.210

AC:

730

AN:

3472

East Asian (EAS)

AF:

0.263

AC:

1362

AN:

5170

South Asian (SAS)

AF:

0.287

AC:

1388

AN:

4830

European-Finnish (FIN)

AF:

0.191

AC:

2024

AN:

10596

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.203

AC:

13829

AN:

67998

Other (OTH)

AF:

0.280

AC:

591

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1565

3130

4696

6261

7826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

434

868

1302

1736

2170

<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:

0.244

Hom.:

5512

Bravo

AF:

0.311

Asia WGS

AF:

0.311

AC:

1086

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

1.7

(source)

DANN

Benign

0.68

PhyloP100

-0.55

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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