rs6117615

chr20-778672-A-Gchr20-778672-A-T

Variant summary

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

The XM_047439868.1(SLC52A3):c.-238+1340T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0765 in 151,886 control chromosomes in the GnomAD database, including 763 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 0.076 (763 hom., cov: 32)
• Consequence: SLC52A3 XM_047439868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

Genes affected

SLC52A3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC52A3	XM_047439868.1	c.-238+1340T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0765 AC: 11613 AN: 151776 Hom.: 763 Cov.: 32

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.0490

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.0765 AC: 11615 AN: 151886 Hom.: 763 Cov.: 32 AF XY: 0.0752 AC XY: 5578 AN XY: 74224

Gnomad4 AFR AF: 0.0787

Gnomad4 AMR AF: 0.0488

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.0286

Gnomad4 FIN AF: 0.0452

Gnomad4 NFE AF: 0.0648

Gnomad4 OTH AF: 0.0721

Alfa AF: 0.0702 Hom.: 899

Bravo AF: 0.0793

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.9
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6117615; hg19: chr20-759315;