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

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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

Gnomad4 AFR exome

AF:

0.131

Gnomad4 AMR exome

AF:

0.257

Gnomad4 ASJ exome

AF:

0.502

Gnomad4 EAS exome

AF:

0.266

Gnomad4 SAS exome

AF:

0.471

Gnomad4 FIN exome

AF:

0.439

Gnomad4 NFE exome

AF:

0.413

Gnomad4 OTH exome

AF:

0.366

GnomAD4 genome

AF:

0.337

AC:

48810

AN:

144810

Hom.:

9622

Cov.:

AF XY:

0.338

AC XY:

23800

AN XY:

70516

show subpopulations

Gnomad4 AFR

AF:

0.155

Gnomad4 AMR

AF:

0.281

Gnomad4 ASJ

AF:

0.493

Gnomad4 EAS

AF:

0.300

Gnomad4 SAS

AF:

0.488

Gnomad4 FIN

AF:

0.413

Gnomad4 NFE

AF:

0.431

Gnomad4 OTH

AF:

0.343

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

DANN

Benign

0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over