19-49441627-C-G

Position:

• chr19-49441627-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439

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]

ACMG classification

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A7	ENST00000600601.5	c.-140+651G>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.337 AC: 48777 AN: 144700 Hom.: 9617 Cov.: 21

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

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.: 21 AF XY: 0.338 AC XY: 23800 AN XY: 70516

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	14
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74174284; hg19: chr19-49944884;