19-49440521-G-A

Position:

• chr19-49440521-G-A

Variant summary

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

The NM_020309.4(SLC17A7):​c.62+797C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,860 control chromosomes in the GnomAD database, including 9,389 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 (9389 hom., cov: 31)
• Consequence: SLC17A7 NM_020309.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC17A7	NM_020309.4	c.62+797C>T		intron_variant		ENST00000221485.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC17A7	ENST00000221485.8	c.62+797C>T		intron_variant		1	NM_020309.4	P1
SLC17A7	ENST00000600601.5	c.-140+1757C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52041 AN: 151742 Hom.: 9386 Cov.: 31

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.399

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.343 AC: 52079 AN: 151860 Hom.: 9389 Cov.: 31 AF XY: 0.337 AC XY: 24978 AN XY: 74222

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.0700

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.393

Alfa AF: 0.350 Hom.: 2329

Bravo AF: 0.353

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.076
DANN	Benign	0.63

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

LitVar

Other links and lift over

dbSNP: rs11672810; hg19: chr19-49943778;