13-98706263-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_005073.4(SLC15A1):c.1150-10T>C variant causes a splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.000645 in 1,610,508 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0033 (2 hom., cov: 32)
  • Exomes 𝑓: 0.00036 (4 hom.)
• Consequence: SLC15A1 NM_005073.4 splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.04437
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.19

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 13-98706263-A-G is Benign according to our data. Variant chr13-98706263-A-G is described in ClinVar as [Benign]. Clinvar id is 719990.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC15A1	NM_005073.4	c.1150-10T>C		splice_polypyrimidine_tract_variant, intron_variant		ENST00000376503.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC15A1	ENST00000376503.10	c.1150-10T>C		splice_polypyrimidine_tract_variant, intron_variant		1	NM_005073.4	P1

Frequencies

GnomAD3 genomes AF: 0.00335 AC: 510 AN: 152218 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00340

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00334

GnomAD3 exomes AF: 0.000983 AC: 244 AN: 248266 Hom.: 0 AF XY: 0.000738 AC XY: 99 AN XY: 134090

Gnomad AFR exome AF: 0.0112

Gnomad AMR exome AF: 0.00119

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000151

Gnomad OTH exome AF: 0.000990

GnomAD4 exome AF: 0.000363 AC: 529 AN: 1458172 Hom.: 4 Cov.: 31 AF XY: 0.000319 AC XY: 231 AN XY: 725270

Gnomad4 AFR exome AF: 0.0102

Gnomad4 AMR exome AF: 0.00127

Gnomad4 ASJ exome AF: 0.0000384

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000441

Gnomad4 OTH exome AF: 0.00138

GnomAD4 genome AF: 0.00335 AC: 510 AN: 152336 Hom.: 2 Cov.: 32 AF XY: 0.00356 AC XY: 265 AN XY: 74486

Gnomad4 AFR AF: 0.0107

Gnomad4 AMR AF: 0.00340

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00255 Hom.: 1

Bravo AF: 0.00383

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

May 24, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	14
Dann	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.044
dbscSNV1_RF	Benign	0.33
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: rs150050510; hg19: chr13-99358517;