rs9582259

Positions:

• chr13-98733736-T-G

Variant summary

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

The NM_005073.4(SLC15A1):​c.5-6877A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0506 in 152,308 control chromosomes in the GnomAD database, including 229 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 0.051 (229 hom., cov: 33)
• Consequence: SLC15A1 NM_005073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823

Genes affected

SLC15A1 (HGNC:10920): (solute carrier family 15 member 1) This gene encodes an intestinal hydrogen peptide cotransporter that is a member of the solute carrier family 15. The encoded protein is localized to the brush border membrane of the intestinal epithelium and mediates the uptake of di- and tripeptides from the lumen into the enterocytes. This protein plays an important role in the uptake and digestion of dietary proteins. This protein also facilitates the absorption of numerous peptidomimetic drugs. [provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC15A1	NM_005073.4	c.5-6877A>C		intron_variant		ENST00000376503.10	NP_005064.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC15A1	ENST00000376503.10	c.5-6877A>C		intron_variant		1	NM_005073.4	ENSP00000365686.4

Frequencies

GnomAD3 genomes AF: 0.0506 AC: 7699 AN: 152190 Hom.: 227 Cov.: 33

Gnomad AFR AF: 0.0596

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0433

Gnomad FIN AF: 0.0369

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0511

Gnomad OTH AF: 0.0473

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0506 AC: 7701 AN: 152308 Hom.: 229 Cov.: 33 AF XY: 0.0492 AC XY: 3663 AN XY: 74474

Gnomad4 AFR AF: 0.0595

Gnomad4 AMR AF: 0.0415

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0432

Gnomad4 FIN AF: 0.0369

Gnomad4 NFE AF: 0.0511

Gnomad4 OTH AF: 0.0477

Alfa AF: 0.0504 Hom.: 286

Bravo AF: 0.0517

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.41

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: rs9582259; hg19: chr13-99385990;