Genetic Variant SLC36A2:c.*63_*76dupTTTTTTTTTTTTTT (chr5-151316740-C-CAAAAAAAAAAAAAA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_181776.3(SLC36A2):c.*63_*76dupTTTTTTTTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SLC36A2
NM_181776.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.985

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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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.63_76dupTTTTTTTTTTTTTT		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.63_76dupTTTTTTTTTTTTTT	3_prime_UTR	Exon 10 of 10	ENSP00000334223.4	Q495M3-1
SLC36A2	ENST00000518280.5	TSL:1	n.986_999dupTTTTTTTTTTTTTT	non_coding_transcript_exon	Exon 9 of 9	ENSP00000428453.1	E5RGH8
SLC36A2	ENST00000518617.5	TSL:1	n.1083_1096dupTTTTTTTTTTTTTT	non_coding_transcript_exon	Exon 10 of 10	ENSP00000430149.1	E5RGH8

Frequencies

GnomAD3 genomes

AF:

0.0000197

AC:

AN:

50738

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

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:

0.0000338

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

845472

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

428970

African (AFR)

AF:

0.00

AC:

AN:

18720

American (AMR)

AF:

0.00

AC:

AN:

21166

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15302

East Asian (EAS)

AF:

0.00

AC:

AN:

24020

South Asian (SAS)

AF:

0.00

AC:

AN:

54540

European-Finnish (FIN)

AF:

0.00

AC:

AN:

26200

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2572

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

647198

Other (OTH)

AF:

0.00

AC:

AN:

35754

GnomAD4 genome

AF:

0.0000197

AC:

AN:

50738

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

22340

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

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:

0.0000338

AC:

AN:

29594

Other (OTH)

AF:

0.00

AC:

AN:

660

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.325

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.98

Splicing

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

Publications

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5-151316740-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over