Variant 19-18594033-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_004750.5(CRLF1):c.1255+32G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 0 hom., cov: 27)

Exomes 𝑓: 0.012 ( 7 hom. )

Failed GnomAD Quality Control

Consequence

CRLF1
NM_004750.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.943

Variant links:

Genes affected

CRLF1 (HGNC:2364): (cytokine receptor like factor 1) This gene encodes a member of the cytokine type I receptor family. The protein forms a secreted complex with cardiotrophin-like cytokine factor 1 and acts on cells expressing ciliary neurotrophic factor receptors. The complex can promote survival of neuronal cells. Mutations in this gene result in Crisponi syndrome and cold-induced sweating syndrome. [provided by RefSeq, Oct 2009]

CRLF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 19-18594033-C-T is Benign according to our data. Variant chr19-18594033-C-T is described in ClinVar as [Benign]. Clinvar id is 1231570.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRLF1	NM_004750.5 linkuse as main transcript	c.1255+32G>A		intron_variant		ENST00000392386.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
CRLF1	ENST00000392386.8 linkuse as main transcript	c.1255+32G>A	intron_variant	1	NM_004750.5	P1
CRLF1	ENST00000684169.1 linkuse as main transcript	c.1260+32G>A	intron_variant
CRLF1	ENST00000594325.1 linkuse as main transcript	n.189+214G>A	intron_variant, non_coding_transcript_variant	3
CRLF1	ENST00000596360.1 linkuse as main transcript	n.70+32G>A	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

221

AN:

92050

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00243

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.00127

Gnomad ASJ

AF:

0.00291

Gnomad EAS

AF:

0.00140

Gnomad SAS

AF:

0.000405

Gnomad FIN

AF:

0.00563

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00240

Gnomad OTH

AF:

0.00328

GnomAD3 exomes

AF:

0.0322

AC:

2838

AN:

88194

Hom.:

AF XY:

0.0294

AC XY:

1435

AN XY:

48856

show subpopulations

Gnomad AFR exome

AF:

0.0417

Gnomad AMR exome

AF:

0.0846

Gnomad ASJ exome

AF:

0.0387

Gnomad EAS exome

AF:

0.0626

Gnomad SAS exome

AF:

0.0264

Gnomad FIN exome

AF:

0.00581

Gnomad NFE exome

AF:

0.0237

Gnomad OTH exome

AF:

0.0407

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0116

AC:

3642

AN:

314630

Hom.:

Cov.:

AF XY:

0.0111

AC XY:

1862

AN XY:

168292

show subpopulations

Gnomad4 AFR exome

AF:

0.0335

Gnomad4 AMR exome

AF:

0.0414

Gnomad4 ASJ exome

AF:

0.0190

Gnomad4 EAS exome

AF:

0.00831

Gnomad4 SAS exome

AF:

0.0107

Gnomad4 FIN exome

AF:

0.00583

Gnomad4 NFE exome

AF:

0.00837

Gnomad4 OTH exome

AF:

0.0132

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00240

AC:

221

AN:

92102

Hom.:

Cov.:

AF XY:

0.00277

AC XY:

120

AN XY:

43332

show subpopulations

Gnomad4 AFR

AF:

0.00242

Gnomad4 AMR

AF:

0.00127

Gnomad4 ASJ

AF:

0.00291

Gnomad4 EAS

AF:

0.00140

Gnomad4 SAS

AF:

0.000404

Gnomad4 FIN

AF:

0.00563

Gnomad4 NFE

AF:

0.00240

Gnomad4 OTH

AF:

0.00325

Alfa

AF:

0.00447

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 23, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

2.1

DANN

Benign

0.95

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over