Genetic Variant SLC17A7:c.-140+651G>C (chr19-49441627-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000600601.5(SLC17A7):c.-140+651G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 200,084 control chromosomes in the GnomAD database, including 14,421 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 0.34 ( 9622 hom., cov: 21)

Exomes 𝑓: 0.41 ( 4799 hom. )

Consequence

SLC17A7
ENST00000600601.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.439

Publications

7 publications found

Variant links:

Genes affected

SLC17A7 (HGNC:16704): (solute carrier family 17 member 7) The protein encoded by this gene is a vesicle-bound, sodium-dependent phosphate transporter that is specifically expressed in the neuron-rich regions of the brain. It is preferentially associated with the membranes of synaptic vesicles and functions in glutamate transport. The protein shares 82% identity with the differentiation-associated Na-dependent inorganic phosphate cotransporter and they appear to form a distinct class within the Na+/Pi cotransporter family. [provided by RefSeq, Jul 2008]

SLC17A7 links:

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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 (SAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC17A7	NM_020309.4 link	c.-248G>C		upstream_gene_variant		ENST00000221485.8	NP_064705.1	Q9P2U7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC17A7	ENST00000600601.5 link	c.-140+651G>C		intron_variant	Intron 1 of 11	2		ENSP00000470338.1		Q9P2U7-2
SLC17A7	ENST00000221485.8 link	c.-248G>C		upstream_gene_variant		1	NM_020309.4	ENSP00000221485.2		Q9P2U7-1

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

48777

AN:

144700

Hom.:

9617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.493

Gnomad EAS

AF:

0.300

Gnomad SAS

AF:

0.487

Gnomad FIN

AF:

0.413

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.431

Gnomad OTH

AF:

0.339

GnomAD4 exome

AF:

0.406

AC:

22425

AN:

55274

Hom.:

4799

AF XY:

0.413

AC XY:

11730

AN XY:

28398

show subpopulations

African (AFR)

AF:

0.131

AC:

139

AN:

1062

American (AMR)

AF:

0.257

AC:

145

AN:

564

Ashkenazi Jewish (ASJ)

AF:

0.502

AC:

281

AN:

560

East Asian (EAS)

AF:

0.266

AC:

181

AN:

680

South Asian (SAS)

AF:

0.471

AC:

468

AN:

994

European-Finnish (FIN)

AF:

0.439

AC:

807

AN:

1840

Middle Eastern (MID)

AF:

0.577

AC:

AN:

156

European-Non Finnish (NFE)

AF:

0.413

AC:

19510

AN:

47222

Other (OTH)

AF:

0.366

AC:

804

AN:

2196

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

659

1318

1978

2637

3296

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

628

1256

1884

2512

3140

<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:

0.337

AC:

48810

AN:

144810

Hom.:

9622

Cov.:

AF XY:

0.338

AC XY:

23800

AN XY:

70516

show subpopulations

African (AFR)

AF:

0.155

AC:

6077

AN:

39136

American (AMR)

AF:

0.281

AC:

4159

AN:

14812

Ashkenazi Jewish (ASJ)

AF:

0.493

AC:

1690

AN:

3426

East Asian (EAS)

AF:

0.300

AC:

1456

AN:

4856

South Asian (SAS)

AF:

0.488

AC:

2217

AN:

4542

European-Finnish (FIN)

AF:

0.413

AC:

3856

AN:

9334

Middle Eastern (MID)

AF:

0.455

AC:

131

AN:

288

European-Non Finnish (NFE)

AF:

0.431

AC:

28277

AN:

65536

Other (OTH)

AF:

0.343

AC:

688

AN:

2004

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.526

Heterozygous variant carriers

1365

2729

4094

5458

6823

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

472

944

1416

1888

2360

<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:

0.255

Hom.:

736

Bravo

AF:

0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

0.44

PromoterAI

-0.070

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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