Variant chr1-151518699-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_020770.3(CGN):c.180C>T(p.Ile60=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00207 in 1,614,132 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0062 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0016 ( 16 hom. )

Consequence

CGN
NM_020770.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.90

Variant links:

Genes affected

CGN (HGNC:17429): (cingulin) Enables cadherin binding activity. Predicted to act upstream of or within bicellular tight junction assembly; epithelial cell morphogenesis; and microtubule cytoskeleton organization. Located in bicellular tight junction and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

CGN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 1-151518699-C-T is Benign according to our data. Variant chr1-151518699-C-T is described in ClinVar as [Benign]. Clinvar id is 711289.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.9 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00625 (951/152244) while in subpopulation AFR AF= 0.0168 (697/41546). AF 95% confidence interval is 0.0157. There are 4 homozygotes in gnomad4. There are 437 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
CGN	NM_020770.3 linkuse as main transcript	c.180C>T	p.Ile60=	synonymous_variant	2/21	ENST00000271636.12	NP_065821.1
CGN	XM_005245365.6 linkuse as main transcript	c.180C>T	p.Ile60=	synonymous_variant	2/21		XP_005245422.1
CGN	XR_921902.3 linkuse as main transcript	n.323C>T		non_coding_transcript_exon_variant	2/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CGN	ENST00000271636.12 linkuse as main transcript	c.180C>T	p.Ile60=	synonymous_variant	2/21	1	NM_020770.3	ENSP00000271636	P1	Q9P2M7-1
CGN	ENST00000502442.1 linkuse as main transcript	c.180C>T	p.Ile60=	synonymous_variant	2/2	1		ENSP00000422299
CGN	ENST00000505188.5 linkuse as main transcript	c.180C>T	p.Ile60=	synonymous_variant	2/2	1		ENSP00000425532
CGN	ENST00000427934.2 linkuse as main transcript	c.180C>T	p.Ile60=	synonymous_variant	3/3	5		ENSP00000410836

Frequencies

GnomAD3 genomes

AF:

0.00617

AC:

939

AN:

152126

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0165

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00144

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.00358

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00248

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00278

AC:

698

AN:

251370

Hom.:

AF XY:

0.00230

AC XY:

312

AN XY:

135860

show subpopulations

Gnomad AFR exome

AF:

0.0161

Gnomad AMR exome

AF:

0.00211

Gnomad ASJ exome

AF:

0.00248

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.000490

Gnomad FIN exome

AF:

0.00370

Gnomad NFE exome

AF:

0.00190

Gnomad OTH exome

AF:

0.00424

GnomAD4 exome

AF:

0.00163

AC:

2389

AN:

1461888

Hom.:

Cov.:

AF XY:

0.00165

AC XY:

1201

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.0160

Gnomad4 AMR exome

AF:

0.00210

Gnomad4 ASJ exome

AF:

0.00207

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000441

Gnomad4 FIN exome

AF:

0.00534

Gnomad4 NFE exome

AF:

0.00107

Gnomad4 OTH exome

AF:

0.00285

GnomAD4 genome

AF:

0.00625

AC:

951

AN:

152244

Hom.:

Cov.:

AF XY:

0.00587

AC XY:

437

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.0168

Gnomad4 AMR

AF:

0.00144

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00358

Gnomad4 NFE

AF:

0.00248

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00350

Hom.:

Bravo

AF:

0.00637

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.00169

EpiControl

AF:

0.00124

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 04, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

1.2

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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