rs10461016

Variant names:

• chr3-45767209-T-C
• rs10461016
• NM_020208.4:c.1099-1468A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020208.4(SLC6A20):​c.1099-1468A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,270 control chromosomes in the GnomAD database, including 630 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 0.082 (630 hom., cov: 33)
• Consequence: SLC6A20 NM_020208.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 5 publications found

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]

SLC6A20 Gene-Disease associations (from GenCC):

• hyperglycinuria

  Inheritance: AR, Unknown Classification: LIMITED, NO_KNOWN Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020208.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A20	NM_020208.4	MANE Select	c.1099-1468A>G		intron	N/A	NP_064593.1
	SLC6A20	NM_001385683.1		c.1132-1468A>G		intron	N/A	NP_001372612.1
	SLC6A20	NM_022405.4		c.988-1468A>G		intron	N/A	NP_071800.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A20	ENST00000358525.9	TSL:1 MANE Select	c.1099-1468A>G		intron	N/A	ENSP00000346298.4
	SLC6A20	ENST00000353278.8	TSL:1	c.988-1468A>G		intron	N/A	ENSP00000296133.5
	SLC6A20	ENST00000473146.5	TSL:1	n.1287-1468A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12447 AN: 152150 Hom.: 630 Cov.: 33

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0739

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0929

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

GnomAD4 genome AF: 0.0817 AC: 12447 AN: 152270 Hom.: 630 Cov.: 33 AF XY: 0.0811 AC XY: 6036 AN XY: 74450

African (AFR) AF: 0.0240 AC: 999 AN: 41564

American (AMR) AF: 0.0847 AC: 1296 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3472

East Asian (EAS) AF: 0.182 AC: 942 AN: 5182

South Asian (SAS) AF: 0.138 AC: 665 AN: 4822

European-Finnish (FIN) AF: 0.0739 AC: 783 AN: 10600

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7132 AN: 68016

Other (OTH) AF: 0.0929 AC: 196 AN: 2110

Alfa AF: 0.0966 Hom.: 1266

Bravo AF: 0.0782

Asia WGS AF: 0.151 AC: 523 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.84
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10461016; hg19: chr3-45808701;