5-151316610-T-C

Position:

• chr5-151316610-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.*207A>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 0.636 in 596,652 control chromosomes in the GnomAD database, including 125,132 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.66 (34387 hom., cov: 28)
  • Exomes 𝑓: 0.63 (90745 hom.)
• Consequence: SLC36A2 NM_181776.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.24

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=-0.99).
• BP6: Variant 5-151316610-T-C is Benign according to our data. Variant chr5-151316610-T-C is described in ClinVar as [Benign]. Clinvar id is 1282405.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC36A2	NM_181776.3	c.*207A>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.*207A>G		3_prime_UTR_variant	10/10	1	NM_181776.3	ENSP00000334223.4

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100534 AN: 151394 Hom.: 34344 Cov.: 28

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.627 AC: 278945 AN: 445144 Hom.: 90745 Cov.: 6 AF XY: 0.634 AC XY: 149216 AN XY: 235212

Gnomad4 AFR exome AF: 0.770

Gnomad4 AMR exome AF: 0.742

Gnomad4 ASJ exome AF: 0.657

Gnomad4 EAS exome AF: 0.989

Gnomad4 SAS exome AF: 0.783

Gnomad4 FIN exome AF: 0.556

Gnomad4 NFE exome AF: 0.560

Gnomad4 OTH exome AF: 0.636

GnomAD4 genome AF: 0.664 AC: 100638 AN: 151508 Hom.: 34387 Cov.: 28 AF XY: 0.669 AC XY: 49530 AN XY: 74012

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.640

Alfa AF: 0.622 Hom.: 3720

Bravo AF: 0.679

Asia WGS AF: 0.885 AC: 3077 AN: 3478

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 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.25

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: rs400878; hg19: chr5-150696171;