rs7006

Variant names:

• chr10-101608897-T-A
• rs7006
• NM_015448.3:c.467T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-101608897-T-A
• chr10-101608897-T-C
• chr10-101608897-T-G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_015448.3(DPCD):​c.467T>A​(p.Leu156*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: DPCD NM_015448.3 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 0 publications found

Genes affected

DPCD (HGNC:24542): (deleted in primary ciliary dyskinesia homolog (mouse)) This gene in mouse encodes a protein that may be involved in the generation and maintenance of ciliated cells. In mouse, expression of this gene increases during ciliated cell differentiation, and disruption of this gene has been linked to primary ciliary dyskinesia. [provided by RefSeq, Jul 2016]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015448.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPCD	NM_015448.3	MANE Select	c.467T>A	p.Leu156*	stop_gained	Exon 5 of 6	NP_056263.1
	DPCD	NM_001329742.2		c.500T>A	p.Leu167*	stop_gained	Exon 5 of 6	NP_001316671.1
	DPCD	NM_001329743.2		c.431T>A	p.Leu144*	stop_gained	Exon 5 of 6	NP_001316672.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPCD	ENST00000370151.9	TSL:1 MANE Select	c.467T>A	p.Leu156*	stop_gained	Exon 5 of 6	ENSP00000359170.4
	DPCD	ENST00000370147.5	TSL:2	c.508T>A	p.Cys170Ser	missense	Exon 6 of 7	ENSP00000359166.1
	DPCD	ENST00000626968.2	TSL:5	c.508T>A	p.Cys170Ser	missense	Exon 6 of 6	ENSP00000486078.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.055	T
BayesDel_noAF	Benign	-0.32
CADD	Pathogenic	26
DANN	Benign	0.96
DEOGEN2	Benign	0.0069	T
Eigen	Benign	0.079
Eigen_PC	Benign	-0.24
FATHMM_MKL	Benign	0.29	N
LIST_S2	Benign	0.34	T
MetaRNN	Benign	0.27	T
MetaSVM	Benign	-0.60	T
PhyloP100		0.60
PROVEAN	Benign	1.0	N
REVEL	Benign	0.026
Sift	Pathogenic	0.0	D
Vest4		0.28
MutPred		0.31		Gain of disorder (P = 0.002)
MVP		0.68
ClinPred		0.53	D
GERP RS		-0.55
Mutation Taster		=33/167	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs7006; hg19: chr10-103368654;