3-45793319-G-T

Variant summary

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

The NM_020208.4(SLC6A20):c.121+2980C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,982 control chromosomes in the GnomAD database, including 2,509 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 0.16 (2509 hom., cov: 32)
• Consequence: SLC6A20 NM_020208.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23

Genes affected

SLC6A20 (HGNC:30927): (solute carrier family 6 member 20) Transport of small hydrophilic substances across cell membranes is mediated by substrate-specific transporter proteins which have been classified into several families of related genes. The protein encoded by this gene belongs to the sodium:neurotransmitter symporter (SNF) family and functions as a proline transporter expressed in kidney and small intestine. Mutations in this gene are associated with Hyperglycinuria and Iminoglycinuria. [provided by RefSeq, Jul 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A20	NM_020208.4	c.121+2980C>A		intron_variant		ENST00000358525.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A20	ENST00000358525.9	c.121+2980C>A		intron_variant		1	NM_020208.4	P1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24476 AN: 151864 Hom.: 2505 Cov.: 32

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.161 AC: 24489 AN: 151982 Hom.: 2509 Cov.: 32 AF XY: 0.165 AC XY: 12259 AN XY: 74258

Gnomad4 AFR AF: 0.0788

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.165

Alfa AF: 0.163 Hom.: 2389

Bravo AF: 0.165

Asia WGS AF: 0.266 AC: 919 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.011
Dann	Benign	0.41

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: rs13064991; hg19: chr3-45834811;