rs4285028

Positions:

• chr3-121941817-A-C
• chr3-121941817-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000489711.6(SLC15A2):​c.*810A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,152 control chromosomes in the GnomAD database, including 4,546 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.22 (4546 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SLC15A2 ENST00000489711.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

Genes affected

SLC15A2 (HGNC:10921): (solute carrier family 15 member 2) The mammalian kidney expresses a proton-coupled peptide transporter that is responsible for the absorption of small peptides, as well as beta-lactam antibiotics and other peptide-like drugs, from the tubular filtrate. This transporter, SLC15A2, belongs to the same gene family as SLC15A1 (MIM 600544), the proton-coupled peptide transporter found in the small intestine (Liu et al, 1995 [PubMed 7756356]).[supplied by OMIM, Feb 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC15A2	NM_021082.4	c.*810A>C		3_prime_UTR_variant	22/22	ENST00000489711.6	NP_066568.3
SLC15A2	NM_001145998.2	c.*810A>C		3_prime_UTR_variant	21/21		NP_001139470.1
SLC15A2	XM_005247722.4	c.*810A>C		3_prime_UTR_variant	21/21		XP_005247779.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC15A2	ENST00000489711.6	c.*810A>C		3_prime_UTR_variant	22/22	1	NM_021082.4	ENSP00000417085	P1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33800 AN: 152032 Hom.: 4541 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.257

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.222 AC: 33813 AN: 152150 Hom.: 4546 Cov.: 32 AF XY: 0.224 AC XY: 16676 AN XY: 74358

Gnomad4 AFR AF: 0.0946

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.0669

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.253

Alfa AF: 0.254 Hom.: 7775

Bravo AF: 0.226

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.37

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: rs4285028; hg19: chr3-121660664;