5-151316740-C-CA

Position:

• chr5-151316740-C-CA

Variant summary

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

The NM_181776.3(SLC36A2):​c.*76dupT 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 0.18 (1102 hom., cov: 0)
  • Exomes 𝑓: 0.16 (87 hom.)
• Consequence: SLC36A2 NM_181776.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.985

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 5-151316740-C-CA is Benign according to our data. Variant chr5-151316740-C-CA is described in ClinVar as [Benign]. Clinvar id is 1242005.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC36A2	NM_181776.3	c.*76dupT		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.*76dupT		3_prime_UTR_variant	10/10	1	NM_181776.3	ENSP00000334223.4

Frequencies

GnomAD3 genomes AF: 0.180 AC: 9125 AN: 50588 Hom.: 1101 Cov.: 0

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.155 AC: 127462 AN: 820606 Hom.: 87 Cov.: 5 AF XY: 0.153 AC XY: 63555 AN XY: 415934

Gnomad4 AFR exome AF: 0.116

Gnomad4 AMR exome AF: 0.105

Gnomad4 ASJ exome AF: 0.145

Gnomad4 EAS exome AF: 0.207

Gnomad4 SAS exome AF: 0.141

Gnomad4 FIN exome AF: 0.127

Gnomad4 NFE exome AF: 0.159

Gnomad4 OTH exome AF: 0.153

GnomAD4 genome AF: 0.180 AC: 9123 AN: 50590 Hom.: 1102 Cov.: 0 AF XY: 0.174 AC XY: 3879 AN XY: 22274

Gnomad4 AFR AF: 0.0882

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.156

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

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: rs33912867; hg19: chr5-150696301;