Genetic Variant SLC36A2:c.*68_*76delTTTTTTTTT (chr5-151316740-CAAAAAAAAA-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_181776.3(SLC36A2):c.*68_*76delTTTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000417 in 896,144 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00034 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00042 ( 3 hom. )

Consequence

SLC36A2
NM_181776.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22

Publications

1 publications found

Variant links:

Genes affected

SLC36A2 (HGNC:18762): (solute carrier family 36 member 2) This gene encodes a pH-dependent proton-coupled amino acid transporter that belongs to the amino acid auxin permease 1 protein family. The encoded protein primarily transports small amino acids such as glycine, alanine and proline. Mutations in this gene are associated with iminoglycinuria and hyperglycinuria. [provided by RefSeq, Sep 2010]

SLC36A2 Gene-Disease associations (from GenCC):

iminoglycinuria
Inheritance: AR, AD Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, ClinGen, Orphanet
hyperglycinuria
Inheritance: SD, AD, AR Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia

SLC36A2 links:

ENSG00000297368 (HGNC:):

ENSG00000297368 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 3 AR,AD,SD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181776.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC36A2	NM_181776.3	MANE Select	c.68_76delTTTTTTTTT		3_prime_UTR	Exon 10 of 10	NP_861441.2	Q495M3-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC36A2	ENST00000335244.9	TSL:1 MANE Select	c.68_76delTTTTTTTTT	3_prime_UTR	Exon 10 of 10	ENSP00000334223.4	Q495M3-1
SLC36A2	ENST00000518280.5	TSL:1	n.991_999delTTTTTTTTT	non_coding_transcript_exon	Exon 9 of 9	ENSP00000428453.1	E5RGH8
SLC36A2	ENST00000518617.5	TSL:1	n.1088_1096delTTTTTTTTT	non_coding_transcript_exon	Exon 10 of 10	ENSP00000430149.1	E5RGH8

Frequencies

GnomAD3 genomes

AF:

0.000335

AC:

AN:

50738

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000265

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000473

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000422

AC:

357

AN:

845406

Hom.:

AF XY:

0.000413

AC XY:

177

AN XY:

428932

show subpopulations

African (AFR)

AF:

0.000160

AC:

AN:

18720

American (AMR)

AF:

0.000142

AC:

AN:

21164

Ashkenazi Jewish (ASJ)

AF:

0.000131

AC:

AN:

15292

East Asian (EAS)

AF:

0.00

AC:

AN:

24020

South Asian (SAS)

AF:

0.000128

AC:

AN:

54526

European-Finnish (FIN)

AF:

0.00

AC:

AN:

26196

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2570

European-Non Finnish (NFE)

AF:

0.000511

AC:

331

AN:

647172

Other (OTH)

AF:

0.000308

AC:

AN:

35746

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000335

AC:

AN:

50738

Hom.:

Cov.:

AF XY:

0.000492

AC XY:

AN XY:

22340

show subpopulations

African (AFR)

AF:

0.000265

AC:

AN:

11304

American (AMR)

AF:

0.00

AC:

AN:

3672

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1712

East Asian (EAS)

AF:

0.00

AC:

AN:

1378

South Asian (SAS)

AF:

0.00

AC:

AN:

1010

European-Finnish (FIN)

AF:

0.00

AC:

AN:

924

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000473

AC:

AN:

29594

Other (OTH)

AF:

0.00

AC:

AN:

660

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.604

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

5-151316740-CAAAAAAAAAAAA-CAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over