2-112652438-A-G

Position:

• chr2-112652438-A-G

Variant summary

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

The NM_005415.5(SLC20A1):​c.562-264A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 498,412 control chromosomes in the GnomAD database, including 28,795 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 0.30 (7752 hom., cov: 32)
  • Exomes 𝑓: 0.32 (21043 hom.)
• Consequence: SLC20A1 NM_005415.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

SLC20A1 (HGNC:10946): (solute carrier family 20 member 1) The protein encoded by this gene is a sodium-phosphate symporter that absorbs phosphate from interstitial fluid for use in cellular functions such as metabolism, signal transduction, and nucleic acid and lipid synthesis. The encoded protein is also a retroviral receptor, causing human cells to be susceptible to infection by gibbon ape leukemia virus, simian sarcoma-associated virus, feline leukemia virus subgroup B, and 10A1 murine leukemia virus.[provided by RefSeq, Mar 2011]

SLC20A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC20A1	NM_005415.5	c.562-264A>G		intron_variant		ENST00000272542.8	NP_005406.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC20A1	ENST00000272542.8	c.562-264A>G		intron_variant		1	NM_005415.5	ENSP00000272542.3

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45676 AN: 151876 Hom.: 7748 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.304

GnomAD4 exome AF: 0.316 AC: 109606 AN: 346420 Hom.: 21043 Cov.: 0 AF XY: 0.318 AC XY: 58229 AN XY: 183058

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.383

Gnomad4 ASJ exome AF: 0.332

Gnomad4 EAS exome AF: 0.798

Gnomad4 SAS exome AF: 0.348

Gnomad4 FIN exome AF: 0.297

Gnomad4 NFE exome AF: 0.260

Gnomad4 OTH exome AF: 0.301

GnomAD4 genome AF: 0.301 AC: 45697 AN: 151992 Hom.: 7752 Cov.: 32 AF XY: 0.307 AC XY: 22772 AN XY: 74280

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.301

Alfa AF: 0.272 Hom.: 8160

Bravo AF: 0.301

Asia WGS AF: 0.535 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.53

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: rs10758; hg19: chr2-113410015;