rs1356031674

Variant names:

• chr1-148960636-TTTGCCGTTTCTTCC-T
• rs1356031674
• NM_001395426.1:c.835-16_835-3delTGCCGTTTCTTCCT

Your query was ambiguous. Multiple possible variants found:

• chr1-148960636-TTTGCCGTTTCTTCC-T
• chr1-148960636-TTTGCCGTTTCTTCC-TTTGCCGTTTCTTCCTTGCCGTTTCTTCC

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001395426.1(PDE4DIP):​c.835-16_835-3delTGCCGTTTCTTCCT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: not found (cov: 8)
• Consequence: PDE4DIP NM_001395426.1 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.13
• Publications: 0 publications found

Genes affected

PDE4DIP (HGNC:15580): (phosphodiesterase 4D interacting protein) The protein encoded by this gene serves to anchor phosphodiesterase 4D to the Golgi/centrosome region of the cell. Defects in this gene may be a cause of myeloproliferative disorder (MBD) associated with eosinophilia. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2010]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP6: Variant 1-148960636-TTTGCCGTTTCTTCC-T is Benign according to our data. Variant chr1-148960636-TTTGCCGTTTCTTCC-T is described in ClinVar as Benign. ClinVar VariationId is 767694.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395426.1. 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
	PDE4DIP	NM_001395426.1	MANE Select	c.835-16_835-3delTGCCGTTTCTTCCT		splice_region intron	N/A	NP_001382355.1	A0A8Q3SI83
	PDE4DIP	NM_001395297.1		c.1126-16_1126-3delTGCCGTTTCTTCCT		splice_region intron	N/A	NP_001382226.1
	PDE4DIP	NM_001350520.2		c.1126-16_1126-3delTGCCGTTTCTTCCT		splice_region intron	N/A	NP_001337449.1	A0A994J5E0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDE4DIP	ENST00000695795.1	MANE Select	c.835-17_835-4delTTGCCGTTTCTTCC		splice_region intron	N/A	ENSP00000512175.1	A0A8Q3SI83
	PDE4DIP	ENST00000369356.8	TSL:1	c.637-17_637-4delTTGCCGTTTCTTCC		splice_region intron	N/A	ENSP00000358363.4	Q5VU43-4
	PDE4DIP	ENST00000369354.7	TSL:1	c.637-17_637-4delTTGCCGTTTCTTCC		splice_region intron	N/A	ENSP00000358360.3	Q5VU43-1

Frequencies

GnomAD3 genomes Cov.: 8

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

GnomAD4 genome Cov.: 8

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs1356031674; hg19: chr1-144923853; COSMIC: COSV57689227; COSMIC: COSV57689227;