Variant 12-9722760-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000327839.4(CLECL1P):n.405G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,613,874 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00085 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0010 ( 2 hom. )

Consequence

CLECL1P
ENST00000327839.4 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.202

Variant links:

Genes affected

CLECL1P (HGNC:24462): (C-type lectin like 1, pseudogene) This gene encodes a type II transmembrane, C-type lectin-like protein that is highly expressed on dendritic and B cells. This protein may act as a T-cell costimulatory molecule that enhances interleukin-4 production, and maybe involved in the regulation of the immune response. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

CLECL1P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004920423).

BP6

Variant 12-9722760-C-A is Benign according to our data. Variant chr12-9722760-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2353151.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLECL1P	NR_172485.1 link	n.402G>T		non_coding_transcript_exon_variant	2/3
CLECL1P	NR_172486.1 link	n.402G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
CLECL1P	ENST00000327839.4 link	n.405G>T	non_coding_transcript_exon_variant	2/2	1
CLECL1P	ENST00000542530.5 link	n.225G>T	non_coding_transcript_exon_variant	2/3	4
CLECL1P	ENST00000621400.5 link	n.316G>T	non_coding_transcript_exon_variant	4/4	5
CLECL1P	ENST00000702603.1 link	n.203G>T	non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes

AF:

0.000854

AC:

130

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000458

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00151

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.000808

AC:

203

AN:

251160

Hom.:

AF XY:

0.000818

AC XY:

111

AN XY:

135778

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.000839

Gnomad ASJ exome

AF:

0.00189

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000785

Gnomad FIN exome

AF:

0.0000925

Gnomad NFE exome

AF:

0.00105

Gnomad OTH exome

AF:

0.000979

GnomAD4 exome

AF:

0.00103

AC:

1510

AN:

1461602

Hom.:

Cov.:

AF XY:

0.00108

AC XY:

785

AN XY:

727102

show subpopulations

Gnomad4 AFR exome

AF:

0.000149

Gnomad4 AMR exome

AF:

0.000738

Gnomad4 ASJ exome

AF:

0.00195

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000905

Gnomad4 FIN exome

AF:

0.000112

Gnomad4 NFE exome

AF:

0.00114

Gnomad4 OTH exome

AF:

0.00103

GnomAD4 genome

AF:

0.000854

AC:

130

AN:

152272

Hom.:

Cov.:

AF XY:

0.000792

AC XY:

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.000241

Gnomad4 AMR

AF:

0.000458

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00151

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.00106

Hom.:

Bravo

AF:

0.000854

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.00104

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00198

AC:

ExAC

AF:

0.000692

AC:

EpiCase

AF:

0.00153

EpiControl

AF:

0.00130

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 01, 2021

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.67

CADD

Benign

1.8

DANN

Benign

0.13

DEOGEN2

Benign

0.0023

.;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.0094

LIST_S2

Benign

0.31

T;T

M_CAP

Benign

0.0021

MetaRNN

Benign

0.0049

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-1.8

.;N

PrimateAI

Benign

0.37

PROVEAN

Benign

0.60

.;N

REVEL

Benign

0.025

Sift

Benign

0.88

.;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

.;B

Vest4

0.052

MutPred

0.34

Gain of catalytic residue at K123 (P = 0.0247);Gain of catalytic residue at K123 (P = 0.0247);

MVP

0.11

MPC

0.19

ClinPred

0.00043

GERP RS

-1.0

Varity_R

0.023

gMVP

0.15

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

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