NM_001165967.2:c.605_607delTGC

Variant names:

• chr17-8121656-GGCA-G
• rs1406071405
• NM_001165967.2:c.605_607delTGC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001165967.2(HES7):​c.605_607delTGC​(p.Leu202del) variant causes a disruptive inframe deletion change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: HES7 NM_001165967.2 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.66

Genes affected

HES7 (HGNC:15977): (hes family bHLH transcription factor 7) This gene encodes a member of the hairy and enhancer of split family of bHLH transcription factors. The mouse ortholog of this gene is regulated by Notch signaling. The protein functions as a transcriptional repressor, and is implicated in correct patterning of the axial skeleton. A mutation in this gene has been shown to result in spondylocostal dysostosis. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HES7	NM_001165967.2	c.605_607delTGC	p.Leu202del	disruptive_inframe_deletion	Exon 4 of 4	ENST00000541682.7	NP_001159439.1
HES7	NM_032580.4	c.590_592delTGC	p.Leu197del	disruptive_inframe_deletion	Exon 4 of 4		NP_115969.2
HES7	XM_047436940.1	c.701_703delTGC	p.Leu234del	disruptive_inframe_deletion	Exon 3 of 3		XP_047292896.1
HES7	XM_047436941.1	c.692_694delTGC	p.Leu231del	disruptive_inframe_deletion	Exon 5 of 5		XP_047292897.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HES7	ENST00000541682.7	c.605_607delTGC	p.Leu202del	disruptive_inframe_deletion	Exon 4 of 4	1	NM_001165967.2	ENSP00000446205.2
HES7	ENST00000317814.8	c.590_592delTGC	p.Leu197del	disruptive_inframe_deletion	Exon 4 of 4	1		ENSP00000314774.4
HES7	ENST00000577735.1	c.*145_*147delTGC		downstream_gene_variant		3		ENSP00000462491.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406071405; hg19: chr17-8024974;