rs7588591

Positions:

• chr2-55191799-C-A
• chr2-55191799-C-G
• chr2-55191799-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000401408.6(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 ENST00000401408.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942

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=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLHC1	NM_152385.4	c.1007-10055G>T		intron_variant		ENST00000401408.6	NP_689598.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLHC1	ENST00000401408.6	c.1007-10055G>T		intron_variant		1	NM_152385.4	ENSP00000384869	P1

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

Gnomad4 AFR AF: 0.993

Gnomad4 AMR AF: 0.988

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.953

Gnomad4 NFE AF: 0.975

Gnomad4 OTH AF: 0.973

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.18

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: rs7588591; hg19: chr2-55418935;