5-151316762-A-AAG

Position:

• chr5-151316762-A-AAG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_181776.3(SLC36A2):​c.*53_*54dupCT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00326 in 1,535,514 control chromosomes in the GnomAD database, including 307 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.024 (283 hom., cov: 29)
  • Exomes 𝑓: 0.0010 (24 hom.)
• Consequence: SLC36A2 NM_181776.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.50

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 -10 ACMG points.

• BP6: Variant 5-151316762-A-AAG is Benign according to our data. Variant chr5-151316762-A-AAG is described in ClinVar as [Benign]. Clinvar id is 1287078.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC36A2	NM_181776.3	c.*53_*54dupCT		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.*53_*54dupCT		3_prime_UTR_variant	10/10	1	NM_181776.3	ENSP00000334223.4

Frequencies

GnomAD3 genomes AF: 0.0243 AC: 3551 AN: 146344 Hom.: 282 Cov.: 29

Gnomad AFR AF: 0.0926

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00693

Gnomad ASJ AF: 0.000868

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00321

Gnomad NFE AF: 0.000325

Gnomad OTH AF: 0.0221

GnomAD4 exome AF: 0.00104 AC: 1450 AN: 1389076 Hom.: 24 Cov.: 25 AF XY: 0.000902 AC XY: 625 AN XY: 692998

Gnomad4 AFR exome AF: 0.0416

Gnomad4 AMR exome AF: 0.00178

Gnomad4 ASJ exome AF: 0.000365

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000758

Gnomad4 FIN exome AF: 0.0000210

Gnomad4 NFE exome AF: 0.0000643

Gnomad4 OTH exome AF: 0.00253

GnomAD4 genome AF: 0.0243 AC: 3557 AN: 146438 Hom.: 283 Cov.: 29 AF XY: 0.0238 AC XY: 1711 AN XY: 71750

Gnomad4 AFR AF: 0.0925

Gnomad4 AMR AF: 0.00692

Gnomad4 ASJ AF: 0.000868

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000325

Gnomad4 OTH AF: 0.0219

Asia WGS AF: 0.00866 AC: 30 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 16, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554096926; hg19: chr5-150696323;