5-151316740-C-CAA

Variant names:

• chr5-151316740-C-CAA
• rs33912867
• NM_181776.3:c.*75_*76dupTT

Variant summary

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

The NM_181776.3(SLC36A2):​c.*75_*76dupTT 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 (1288 hom., cov: 0)
  • Exomes 𝑓: 0.11 (91 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-CAA is Benign according to our data. Variant chr5-151316740-C-CAA is described in ClinVar as [Benign]. Clinvar id is 1244915.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC36A2	NM_181776.3	c.*75_*76dupTT		3_prime_UTR_variant	Exon 10 of 10	ENST00000335244.9	NP_861441.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC36A2	ENST00000335244	c.*75_*76dupTT		3_prime_UTR_variant	Exon 10 of 10	1	NM_181776.3	ENSP00000334223.4

Frequencies

GnomAD3 genomes AF: 0.180 AC: 8995 AN: 50094 Hom.: 1285 Cov.: 0

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.182

GnomAD4 exome AF: 0.112 AC: 89885 AN: 803216 Hom.: 91 Cov.: 5 AF XY: 0.111 AC XY: 45015 AN XY: 407072

Gnomad4 AFR exome AF: 0.174

Gnomad4 AMR exome AF: 0.131

Gnomad4 ASJ exome AF: 0.0979

Gnomad4 EAS exome AF: 0.141

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.0870

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.117

GnomAD4 genome AF: 0.180 AC: 9005 AN: 50096 Hom.: 1288 Cov.: 0 AF XY: 0.182 AC XY: 4012 AN XY: 22086

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.181

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 15, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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: rs33912867; hg19: chr5-150696301;