rs10772915

Positions:

• chr12-16253756-G-A
• chr12-16253756-G-C

Variant summary

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

The NM_001170798.1(SLC15A5):​c.754+3945C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,894 control chromosomes in the GnomAD database, including 15,514 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 0.45 (15514 hom., cov: 31)
• Consequence: SLC15A5 NM_001170798.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

SLC15A5 (HGNC:33455): (solute carrier family 15 member 5) Predicted to enable symporter activity. Predicted to be involved in peptide transport; protein transport; and transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC101928362 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC15A5	NM_001170798.1	c.754+3945C>T		intron_variant		ENST00000344941.3	NP_001164269.1
LOC101928362	XR_001749028.1	n.526+8733G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC15A5	ENST00000344941.3	c.754+3945C>T		intron_variant		5	NM_001170798.1	ENSP00000340402.3

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68133 AN: 151776 Hom.: 15501 Cov.: 31

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.449 AC: 68177 AN: 151894 Hom.: 15514 Cov.: 31 AF XY: 0.449 AC XY: 33318 AN XY: 74232

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.423

Alfa AF: 0.428 Hom.: 8461

Bravo AF: 0.449

Asia WGS AF: 0.511 AC: 1777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.43

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: rs10772915; hg19: chr12-16406690;