rs7588591

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-55191799-C-A
• chr2-55191799-C-G
• chr2-55191799-C-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.1007-10055G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.976 in 151,466 control chromosomes in the GnomAD database, including 72,196 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 0.98 (72196 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.985 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.1007-10055G>T		intron	N/A	NP_689598.2	Q8NHS4-1
	CLHC1	NM_001353780.2		c.809-10055G>T		intron	N/A	NP_001340709.1
	CLHC1	NM_001135598.2		c.641-10055G>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.1007-10055G>T		intron	N/A	ENSP00000384869.1	Q8NHS4-1
	CLHC1	ENST00000406076.5	TSL:1	c.641-10055G>T		intron	N/A	ENSP00000385512.1	Q8NHS4-2
	CLHC1	ENST00000407122.5	TSL:5	c.1007-10055G>T		intron	N/A	ENSP00000385778.1	Q8NHS4-1

Frequencies

GnomAD3 genomes AF: 0.976 AC: 147741 AN: 151350 Hom.: 72141 Cov.: 28

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.988

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.953

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.975

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.976 AC: 147854 AN: 151466 Hom.: 72196 Cov.: 28 AF XY: 0.975 AC XY: 72146 AN XY: 74012

African (AFR) AF: 0.993 AC: 41025 AN: 41326

American (AMR) AF: 0.988 AC: 15025 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3173 AN: 3466

East Asian (EAS) AF: 0.976 AC: 5034 AN: 5158

South Asian (SAS) AF: 0.900 AC: 4320 AN: 4798

European-Finnish (FIN) AF: 0.953 AC: 9920 AN: 10412

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.975 AC: 66126 AN: 67794

Other (OTH) AF: 0.973 AC: 2038 AN: 2094

Alfa AF: 0.976 Hom.: 2318

Bravo AF: 0.981

Asia WGS AF: 0.935 AC: 3250 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.18
PhyloP100		-0.94
Mutation Taster		=100/0	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: rs7588591; hg19: chr2-55418935;