5-151316610-T-C

Variant names:

• chr5-151316610-T-C
• rs400878
• NM_181776.3:c.*207A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

SLC36A2 Gene-Disease associations (from GenCC):

• iminoglycinuria

  Inheritance: AR, AD Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, ClinGen, Orphanet
• hyperglycinuria

  Inheritance: SD, AD, AR Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia

ENSG00000297368 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181776.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC36A2	NM_181776.3	MANE Select	c.*207A>G		3_prime_UTR	Exon 10 of 10	NP_861441.2	Q495M3-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC36A2	ENST00000335244.9	TSL:1 MANE Select	c.*207A>G		3_prime_UTR	Exon 10 of 10	ENSP00000334223.4	Q495M3-1
	SLC36A2	ENST00000518280.5	TSL:1	n.*1130A>G		non_coding_transcript_exon	Exon 9 of 9	ENSP00000428453.1	E5RGH8
	SLC36A2	ENST00000518617.5	TSL:1	n.*1227A>G		non_coding_transcript_exon	Exon 10 of 10	ENSP00000430149.1	E5RGH8

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

African (AFR) AF: 0.770 AC: 9466 AN: 12296

American (AMR) AF: 0.742 AC: 12430 AN: 16746

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 8207 AN: 12494

East Asian (EAS) AF: 0.989 AC: 25408 AN: 25690

South Asian (SAS) AF: 0.783 AC: 34484 AN: 44016

European-Finnish (FIN) AF: 0.556 AC: 12616 AN: 22678

Middle Eastern (MID) AF: 0.662 AC: 1192 AN: 1800

European-Non Finnish (NFE) AF: 0.560 AC: 159621 AN: 285004

Other (OTH) AF: 0.636 AC: 15521 AN: 24420

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

African (AFR) AF: 0.772 AC: 31851 AN: 41276

American (AMR) AF: 0.705 AC: 10746 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2303 AN: 3466

East Asian (EAS) AF: 0.983 AC: 5062 AN: 5150

South Asian (SAS) AF: 0.802 AC: 3844 AN: 4792

European-Finnish (FIN) AF: 0.555 AC: 5812 AN: 10470

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38760 AN: 67816

Other (OTH) AF: 0.640 AC: 1346 AN: 2102

Alfa AF: 0.628 Hom.: 3948

Bravo AF: 0.679

Asia WGS AF: 0.885 AC: 3077 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.25
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs400878; hg19: chr5-150696171;