Variant 5-151316740-C-CAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_181776.3(SLC36A2):c.*74_*76dupTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 1709 hom., cov: 0)

Exomes 𝑓: 0.10 ( 124 hom. )

Consequence

SLC36A2
NM_181776.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.985

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-151316740-C-CAAA is Benign according to our data. Variant chr5-151316740-C-CAAA is described in ClinVar as [Benign]. Clinvar id is 1179293.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC36A2	NM_181776.3 linkuse as main transcript	c.74_76dupTTT		3_prime_UTR_variant	10/10	ENST00000335244.9	NP_861441.2	Q495M3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC36A2	ENST00000335244.9 linkuse as main transcript	c.74_76dupTTT		3_prime_UTR_variant	10/10	1	NM_181776.3	ENSP00000334223.4		Q495M3-1

Frequencies

GnomAD3 genomes

AF:

0.244

AC:

12249

AN:

50278

Hom.:

1709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.383

Gnomad AMR

AF:

0.246

Gnomad ASJ

AF:

0.295

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.243

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.231

GnomAD4 exome

AF:

0.103

AC:

82658

AN:

799822

Hom.:

124

Cov.:

AF XY:

0.103

AC XY:

41620

AN XY:

404784

show subpopulations

Gnomad4 AFR exome

AF:

0.0799

Gnomad4 AMR exome

AF:

0.101

Gnomad4 ASJ exome

AF:

0.0913

Gnomad4 EAS exome

AF:

0.119

Gnomad4 SAS exome

AF:

0.109

Gnomad4 FIN exome

AF:

0.0659

Gnomad4 NFE exome

AF:

0.105

Gnomad4 OTH exome

AF:

0.109

GnomAD4 genome

AF:

0.244

AC:

12247

AN:

50280

Hom.:

1709

Cov.:

AF XY:

0.236

AC XY:

5213

AN XY:

22126

show subpopulations

Gnomad4 AFR

AF:

0.123

Gnomad4 AMR

AF:

0.246

Gnomad4 ASJ

AF:

0.295

Gnomad4 EAS

AF:

0.251

Gnomad4 SAS

AF:

0.254

Gnomad4 FIN

AF:

0.107

Gnomad4 NFE

AF:

0.288

Gnomad4 OTH

AF:

0.231

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over