rs2043714

Variant names:

• chr2-55220596-G-A
• rs2043714
• NM_152385.4:c.177+1639C>T

Variant summary

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

The NM_152385.4(CLHC1):​c.177+1639C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 152,236 control chromosomes in the GnomAD database, including 68,806 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 0.95 (68806 hom., cov: 31)
• Consequence: CLHC1 NM_152385.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

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.177+1639C>T		intron	N/A	NP_689598.2	Q8NHS4-1
	CLHC1	NM_001353780.2		c.177+1639C>T		intron	N/A	NP_001340709.1
	CLHC1	NM_001135598.2		c.-189-2598C>T		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.177+1639C>T		intron	N/A	ENSP00000384869.1	Q8NHS4-1
	CLHC1	ENST00000406076.5	TSL:1	c.-189-2598C>T		intron	N/A	ENSP00000385512.1	Q8NHS4-2
	CLHC1	ENST00000407122.5	TSL:5	c.177+1639C>T		intron	N/A	ENSP00000385778.1	Q8NHS4-1

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144546 AN: 152118 Hom.: 68773 Cov.: 31

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.975

Gnomad OTH AF: 0.954

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

GnomAD4 genome AF: 0.950 AC: 144635 AN: 152236 Hom.: 68806 Cov.: 31 AF XY: 0.949 AC XY: 70676 AN XY: 74436

African (AFR) AF: 0.900 AC: 37369 AN: 41510

American (AMR) AF: 0.980 AC: 14984 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3177 AN: 3470

East Asian (EAS) AF: 0.979 AC: 5080 AN: 5190

South Asian (SAS) AF: 0.901 AC: 4341 AN: 4820

European-Finnish (FIN) AF: 0.954 AC: 10125 AN: 10608

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.975 AC: 66356 AN: 68028

Other (OTH) AF: 0.954 AC: 2012 AN: 2108

Alfa AF: 0.965 Hom.: 11798

Bravo AF: 0.951

Asia WGS AF: 0.931 AC: 3232 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.5
DANN	Benign	0.78
PhyloP100		0.029
Mutation Taster		=99/1	polymorphism (auto)

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: rs2043714; hg19: chr2-55447732;