3-45762577-C-T

Position:

• chr3-45762577-C-T

Variant summary

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

The NM_020208.4(SLC6A20):​c.1463+336G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 152,176 control chromosomes in the GnomAD database, including 25,575 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 0.57 (25575 hom., cov: 33)
• Consequence: SLC6A20 NM_020208.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.892

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A20	NM_020208.4	c.1463+336G>A		intron_variant		ENST00000358525.9	NP_064593.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A20	ENST00000358525.9	c.1463+336G>A		intron_variant		1	NM_020208.4	ENSP00000346298	P1

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86255 AN: 152058 Hom.: 25582 Cov.: 33

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.567 AC: 86277 AN: 152176 Hom.: 25575 Cov.: 33 AF XY: 0.576 AC XY: 42838 AN XY: 74396

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.583

Alfa AF: 0.628 Hom.: 41047

Bravo AF: 0.553

Asia WGS AF: 0.587 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
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: rs2286489; hg19: chr3-45804069;