19-49429505-G-T

Variant names:

• chr19-49429505-G-T
• rs1043558
• NM_020309.4:c.*1014C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020309.4(SLC17A7):​c.*1014C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 398,776 control chromosomes in the GnomAD database, including 110,083 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 0.76 (44782 hom., cov: 31)
  • Exomes 𝑓: 0.72 (65301 hom.)
• Consequence: SLC17A7 NM_020309.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 8 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020309.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A7	NM_020309.4	MANE Select	c.*1014C>A		3_prime_UTR	Exon 12 of 12	NP_064705.1	Q9P2U7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A7	ENST00000221485.8	TSL:1 MANE Select	c.*1014C>A		3_prime_UTR	Exon 12 of 12	ENSP00000221485.2	Q9P2U7-1
	SLC17A7	ENST00000969901.1		c.*1014C>A		3_prime_UTR	Exon 13 of 13	ENSP00000639960.1
	SLC17A7	ENST00000969902.1		c.*1014C>A		3_prime_UTR	Exon 12 of 12	ENSP00000639961.1

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115766 AN: 151906 Hom.: 44739 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.767

GnomAD4 exome AF: 0.721 AC: 177897 AN: 246752 Hom.: 65301 Cov.: 0 AF XY: 0.722 AC XY: 90259 AN XY: 125078

African (AFR) AF: 0.863 AC: 6193 AN: 7180

American (AMR) AF: 0.661 AC: 4917 AN: 7434

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 7173 AN: 9240

East Asian (EAS) AF: 0.472 AC: 10809 AN: 22892

South Asian (SAS) AF: 0.775 AC: 2351 AN: 3034

European-Finnish (FIN) AF: 0.635 AC: 13499 AN: 21252

Middle Eastern (MID) AF: 0.873 AC: 1130 AN: 1294

European-Non Finnish (NFE) AF: 0.756 AC: 119534 AN: 158054

Other (OTH) AF: 0.751 AC: 12291 AN: 16372

GnomAD4 genome AF: 0.762 AC: 115861 AN: 152024 Hom.: 44782 Cov.: 31 AF XY: 0.755 AC XY: 56091 AN XY: 74298

African (AFR) AF: 0.866 AC: 35920 AN: 41482

American (AMR) AF: 0.704 AC: 10761 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2744 AN: 3472

East Asian (EAS) AF: 0.436 AC: 2247 AN: 5154

South Asian (SAS) AF: 0.787 AC: 3789 AN: 4814

European-Finnish (FIN) AF: 0.636 AC: 6720 AN: 10562

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51037 AN: 67946

Other (OTH) AF: 0.768 AC: 1622 AN: 2112

Alfa AF: 0.754 Hom.: 42948

Bravo AF: 0.766

Asia WGS AF: 0.665 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.59
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1043558; hg19: chr19-49932762;