rs2043714

chr2-55220596-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLHC1	NM_152385.4	c.177+1639C>T		intron_variant		ENST00000401408.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLHC1	ENST00000401408.6	c.177+1639C>T		intron_variant		1	NM_152385.4	P1

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

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.980

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.954

Gnomad4 NFE AF: 0.975

Gnomad4 OTH AF: 0.954

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	6.5
Dann	Benign	0.78

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

Publications

LitVar

Other links and lift over

dbSNP: rs2043714; hg19: chr2-55447732;