7-153855979-A-T

Position:

• chr7-153855979-A-T

Variant summary

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

The XR_001745002.1(LOC107986722):​n.701A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,144 control chromosomes in the GnomAD database, including 2,779 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 (2779 hom., cov: 32)
• Consequence: LOC107986722 XR_001745002.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986722	XR_001745002.1	n.701A>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPP6	ENST00000706130.1	c.60+106971A>T		intron_variant				ENSP00000516215

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28613 AN: 152026 Hom.: 2779 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.188 AC: 28628 AN: 152144 Hom.: 2779 Cov.: 32 AF XY: 0.184 AC XY: 13725 AN XY: 74408

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.198

Alfa AF: 0.0659 Hom.: 101

Bravo AF: 0.189

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6947495; hg19: chr7-153553064;