2-55191799-C-G

Variant names:

• chr2-55191799-C-G
• rs7588591
• NM_152385.4:c.1007-10055G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_152385.4(CLHC1):​c.1007-10055G>C variant causes a intron 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: 28)
• Consequence: CLHC1 NM_152385.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 1 publications found

Genes affected

CLHC1 (HGNC:26453): (clathrin heavy chain linker domain containing 1)

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152385.4. 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
	CLHC1	NM_152385.4	MANE Select	c.1007-10055G>C		intron	N/A	NP_689598.2	Q8NHS4-1
	CLHC1	NM_001353780.2		c.809-10055G>C		intron	N/A	NP_001340709.1
	CLHC1	NM_001135598.2		c.641-10055G>C		intron	N/A	NP_001129070.1	Q8NHS4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLHC1	ENST00000401408.6	TSL:1 MANE Select	c.1007-10055G>C		intron	N/A	ENSP00000384869.1	Q8NHS4-1
	CLHC1	ENST00000406076.5	TSL:1	c.641-10055G>C		intron	N/A	ENSP00000385512.1	Q8NHS4-2
	CLHC1	ENST00000407122.5	TSL:5	c.1007-10055G>C		intron	N/A	ENSP00000385778.1	Q8NHS4-1

Frequencies

GnomAD3 genomes Cov.: 28

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

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.33
DANN	Benign	0.078
PhyloP100		-0.94

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: rs7588591; hg19: chr2-55418935;