chr8-42449295-T-C

Position:

• chr8-42449295-T-C

Variant summary

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

The NM_001257180.2(SLC20A2):​c.614-4533A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,098 control chromosomes in the GnomAD database, including 9,316 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 0.23 (9316 hom., cov: 32)
• Consequence: SLC20A2 NM_001257180.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

Genes affected

SLC20A2 (HGNC:10947): (solute carrier family 20 member 2) This gene encodes a member of the inorganic phosphate transporter family. The encoded protein is a type 3 sodium-dependent phosphate symporter that plays an important role in phosphate homeostasis by mediating cellular phosphate uptake. The encoded protein also confers susceptibility to viral infection as a gamma-retroviral receptor. Mutations in this gene may play a role in familial idiopathic basal ganglia calcification. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Mar 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC20A2	NM_001257180.2	c.614-4533A>G		intron_variant		ENST00000520262.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC20A2	ENST00000520262.6	c.614-4533A>G		intron_variant		2	NM_001257180.2	P1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34645 AN: 151980 Hom.: 9269 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0459

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0448

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.228 AC: 34754 AN: 152098 Hom.: 9316 Cov.: 32 AF XY: 0.225 AC XY: 16703 AN XY: 74336

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0459

Gnomad4 NFE AF: 0.0448

Gnomad4 OTH AF: 0.198

Alfa AF: 0.0705 Hom.: 410

Bravo AF: 0.248

Asia WGS AF: 0.241 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.27

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: rs7832529; hg19: chr8-42306813;