rs12671878

chr7-153861864-C-Achr7-153861864-C-T

Variant summary

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

The XR_001745002.1(LOC107986722):n.3346-3042C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,154 control chromosomes in the GnomAD database, including 2,902 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 (2902 hom., cov: 33)
• Consequence: LOC107986722 XR_001745002.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

Genes affected

LOC107986722 (HGNC:):

DPP6 (HGNC:3010): (dipeptidyl peptidase like 6) This gene encodes a single-pass type II membrane protein that is a member of the peptidase S9B family of serine proteases. This protein has no detectable protease activity, most likely due to the absence of the conserved serine residue normally present in the catalytic domain of serine proteases. However, it does bind specific voltage-gated potassium channels and alters their expression and biophysical properties. Variations in this gene may be associated with susceptibility to amyotrophic lateral sclerosis and with idiopathic ventricular fibrillation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986722	XR_001745002.1	n.3346-3042C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP6	ENST00000706130.1	c.60+112856C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29411 AN: 152034 Hom.: 2901 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.193 AC: 29432 AN: 152154 Hom.: 2902 Cov.: 33 AF XY: 0.189 AC XY: 14062 AN XY: 74394

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.207

Alfa AF: 0.201 Hom.: 4294

Bravo AF: 0.198

Asia WGS AF: 0.210 AC: 728 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.65
Dann	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12671878; hg19: chr7-153558949;