chr7-154630460-C-T

Variant names:

• chr7-154630460-C-T
• rs6956703
• NM_130797.4:c.628-7361C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_130797.4(DPP6):​c.628-7361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,052 control chromosomes in the GnomAD database, including 14,307 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 0.42 (14307 hom., cov: 33)
• Consequence: DPP6 NM_130797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 3 publications found

Genes affected

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]

DPP6 Gene-Disease associations (from GenCC):

• autosomal dominant primary microcephaly

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• paroxysmal familial ventricular fibrillation

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• ventricular fibrillation, paroxysmal familial, 2

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• intellectual disability, autosomal dominant 33

  Inheritance: Unknown, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• complex neurodevelopmental disorder

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130797.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP6	NM_130797.4	MANE Select	c.628-7361C>T		intron	N/A	NP_570629.2	P42658-1
	DPP6	NM_001364497.2		c.445-7361C>T		intron	N/A	NP_001351426.1	A0A994J7K0
	DPP6	NM_001364498.2		c.445-7361C>T		intron	N/A	NP_001351427.1	A0A994J7K0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP6	ENST00000377770.8	TSL:1 MANE Select	c.628-7361C>T		intron	N/A	ENSP00000367001.3	P42658-1
	DPP6	ENST00000332007.7	TSL:1	c.442-7361C>T		intron	N/A	ENSP00000328226.3	P42658-2
	DPP6	ENST00000404039.5	TSL:1	c.436-7361C>T		intron	N/A	ENSP00000385578.1	E9PF59

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64402 AN: 151934 Hom.: 14284 Cov.: 33

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.424 AC: 64467 AN: 152052 Hom.: 14307 Cov.: 33 AF XY: 0.421 AC XY: 31317 AN XY: 74318

African (AFR) AF: 0.572 AC: 23712 AN: 41470

American (AMR) AF: 0.341 AC: 5214 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1323 AN: 3464

East Asian (EAS) AF: 0.235 AC: 1216 AN: 5168

South Asian (SAS) AF: 0.279 AC: 1348 AN: 4824

European-Finnish (FIN) AF: 0.442 AC: 4662 AN: 10558

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25616 AN: 67982

Other (OTH) AF: 0.408 AC: 861 AN: 2108

Alfa AF: 0.384 Hom.: 7438

Bravo AF: 0.424

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.33
PhyloP100		-0.38

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

Other links and lift over

dbSNP: rs6956703; hg19: chr7-154422170; COSMIC: COSV59609777;