5-151316704-T-C

Position:

• chr5-151316704-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_181776.3(SLC36A2):​c.*113A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0484 in 1,294,132 control chromosomes in the GnomAD database, including 2,308 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.089 (727 hom., cov: 23)
  • Exomes 𝑓: 0.044 (1581 hom.)
• Consequence: SLC36A2 NM_181776.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.695

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant 5-151316704-T-C is Benign according to our data. Variant chr5-151316704-T-C is described in ClinVar as [Benign]. Clinvar id is 1222845.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC36A2	NM_181776.3	c.*113A>G		3_prime_UTR_variant	10/10	ENST00000335244.9	NP_861441.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC36A2	ENST00000335244.9	c.*113A>G		3_prime_UTR_variant	10/10	1	NM_181776.3	ENSP00000334223.4

Frequencies

GnomAD3 genomes AF: 0.0887 AC: 11502 AN: 129662 Hom.: 723 Cov.: 23

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.0737

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.0696

GnomAD4 exome AF: 0.0439 AC: 51146 AN: 1164386 Hom.: 1581 Cov.: 16 AF XY: 0.0445 AC XY: 26037 AN XY: 585306

Gnomad4 AFR exome AF: 0.172

Gnomad4 AMR exome AF: 0.0270

Gnomad4 ASJ exome AF: 0.0185

Gnomad4 EAS exome AF: 0.0926

Gnomad4 SAS exome AF: 0.0689

Gnomad4 FIN exome AF: 0.0544

Gnomad4 NFE exome AF: 0.0369

Gnomad4 OTH exome AF: 0.0513

GnomAD4 genome AF: 0.0889 AC: 11533 AN: 129746 Hom.: 727 Cov.: 23 AF XY: 0.0928 AC XY: 5624 AN XY: 60628

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0641

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.0789

Gnomad4 FIN AF: 0.0921

Gnomad4 NFE AF: 0.0390

Gnomad4 OTH AF: 0.0737

Alfa AF: 0.0614 Hom.: 56

Bravo AF: 0.0832

Asia WGS AF: 0.118 AC: 409 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.27

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: rs10045447; hg19: chr5-150696265;