Menu
GeneBe

13-98706224-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_005073.4(SLC15A1):c.1179C>T(p.Asn393=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 1,613,230 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0082 ( 27 hom., cov: 32)
Exomes 𝑓: 0.00093 ( 19 hom. )

Consequence

SLC15A1
NM_005073.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.39
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 13-98706224-G-A is Benign according to our data. Variant chr13-98706224-G-A is described in ClinVar as [Benign]. Clinvar id is 776807.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.39 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00824 (1255/152248) while in subpopulation AFR AF= 0.0287 (1192/41526). AF 95% confidence interval is 0.0274. There are 27 homozygotes in gnomad4. There are 597 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 27 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC15A1NM_005073.4 linkuse as main transcriptc.1179C>T p.Asn393= synonymous_variant 16/23 ENST00000376503.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC15A1ENST00000376503.10 linkuse as main transcriptc.1179C>T p.Asn393= synonymous_variant 16/231 NM_005073.4 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00824
AC:
1253
AN:
152130
Hom.:
27
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0287
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00216
Gnomad ASJ
AF:
0.00144
Gnomad EAS
AF:
0.000577
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.00574
GnomAD3 exomes
AF:
0.00224
AC:
560
AN:
250384
Hom.:
9
AF XY:
0.00180
AC XY:
243
AN XY:
135290
show subpopulations
Gnomad AFR exome
AF:
0.0283
Gnomad AMR exome
AF:
0.00102
Gnomad ASJ exome
AF:
0.00378
Gnomad EAS exome
AF:
0.000218
Gnomad SAS exome
AF:
0.0000989
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000115
Gnomad OTH exome
AF:
0.00115
GnomAD4 exome
AF:
0.000933
AC:
1363
AN:
1460982
Hom.:
19
Cov.:
31
AF XY:
0.000791
AC XY:
575
AN XY:
726774
show subpopulations
Gnomad4 AFR exome
AF:
0.0299
Gnomad4 AMR exome
AF:
0.00135
Gnomad4 ASJ exome
AF:
0.00314
Gnomad4 EAS exome
AF:
0.0000757
Gnomad4 SAS exome
AF:
0.0000813
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000774
Gnomad4 OTH exome
AF:
0.00196
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00824
AC:
1255
AN:
152248
Hom.:
27
Cov.:
32
AF XY:
0.00802
AC XY:
597
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0287
Gnomad4 AMR
AF:
0.00216
Gnomad4 ASJ
AF:
0.00144
Gnomad4 EAS
AF:
0.000578
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.00568
Alfa
AF:
0.00136
Hom.:
6
Bravo
AF:
0.00947
Asia WGS
AF:
0.00173
AC:
6
AN:
3478
EpiCase
AF:
0.000164
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 17, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
0.17
Dann
Benign
0.45

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8187836; hg19: chr13-99358478; API