19-49441627-C-T

Variant names:

• chr19-49441627-C-T
• rs74174284
• ENST00000600601.5:c.-140+651G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000600601.5(SLC17A7):​c.-140+651G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 21)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC17A7 ENST00000600601.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439
• Publications: 7 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 21

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 55538 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 28534

African (AFR) AF: 0.00 AC: 0 AN: 1064

American (AMR) AF: 0.00 AC: 0 AN: 568

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 572

East Asian (EAS) AF: 0.00 AC: 0 AN: 684

South Asian (SAS) AF: 0.00 AC: 0 AN: 1000

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1846

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 156

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 47442

Other (OTH) AF: 0.00 AC: 0 AN: 2206

GnomAD4 genome Cov.: 21

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	14
DANN	Benign	0.87
PhyloP100		0.44
PromoterAI		-0.073	Neutral

Splicing

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

Other links and lift over

dbSNP: rs74174284; hg19: chr19-49944884;