NM_005073.4:c.5-6877A>C

Variant names:

• chr13-98733736-T-G
• rs9582259
• NM_005073.4:c.5-6877A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005073.4. 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
	SLC15A1	NM_005073.4	MANE Select	c.5-6877A>C		intron	N/A	NP_005064.1	P46059

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC15A1	ENST00000376503.10	TSL:1 MANE Select	c.5-6877A>C		intron	N/A	ENSP00000365686.4	P46059
	SLC15A1	ENST00000856774.1		c.5-6877A>C		intron	N/A	ENSP00000526834.1

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

African (AFR) AF: 0.0595 AC: 2474 AN: 41570

American (AMR) AF: 0.0415 AC: 635 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.0432 AC: 208 AN: 4818

European-Finnish (FIN) AF: 0.0369 AC: 392 AN: 10624

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0511 AC: 3477 AN: 68024

Other (OTH) AF: 0.0477 AC: 101 AN: 2116

Alfa AF: 0.0497 Hom.: 672

Bravo AF: 0.0517

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.41
PhyloP100		-0.82
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: rs9582259; hg19: chr13-99385990;