chr13-98684036-C-T

Variant names:

• chr13-98684036-C-T
• rs1289389
• NM_005073.4:c.*688G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005073.4(SLC15A1):​c.*688G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,044 control chromosomes in the GnomAD database, including 2,918 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 0.19 (2916 hom., cov: 32)
  • Exomes 𝑓: 0.38 (2 hom.)
• Consequence: SLC15A1 NM_005073.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 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.*688G>A		3_prime_UTR	Exon 23 of 23	NP_005064.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC15A1	ENST00000376503.10	TSL:1 MANE Select	c.*688G>A		3_prime_UTR	Exon 23 of 23	ENSP00000365686.4
	SLC15A1	ENST00000856774.1		c.*688G>A		3_prime_UTR	Exon 21 of 21	ENSP00000526834.1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28318 AN: 151910 Hom.: 2913 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.375 AC: 6 AN: 16 Hom.: 2 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 4 AN: 12

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.186 AC: 28320 AN: 152028 Hom.: 2916 Cov.: 32 AF XY: 0.185 AC XY: 13743 AN XY: 74292

African (AFR) AF: 0.121 AC: 5019 AN: 41468

American (AMR) AF: 0.137 AC: 2085 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1225 AN: 5168

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1821 AN: 10528

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15672 AN: 67992

Other (OTH) AF: 0.183 AC: 385 AN: 2108

Alfa AF: 0.211 Hom.: 11261

Bravo AF: 0.180

Asia WGS AF: 0.206 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.57
PhyloP100		0.27
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: rs1289389; hg19: chr13-99336290;