chr15-57475784-G-T

Variant names:

• chr15-57475784-G-T
• rs2922219
• NM_032866.5:c.2403+13892G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032866.5(CGNL1):​c.2403+13892G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 151,856 control chromosomes in the GnomAD database, including 49,703 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 0.81 (49703 hom., cov: 29)
• Consequence: CGNL1 NM_032866.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 6 publications found

Genes affected

CGNL1 (HGNC:25931): (cingulin like 1) This gene encodes a member of the cingulin family. The encoded protein localizes to both adherens and tight cell-cell junctions and mediates junction assembly and maintenance by regulating the activity of the small GTPases RhoA and Rac1. Heterozygous chromosomal rearrangements resulting in association of the promoter for this gene with the aromatase gene are a cause of aromatase excess syndrome. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Nov 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032866.5. 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
	CGNL1	NM_032866.5	MANE Select	c.2403+13892G>T		intron	N/A	NP_116255.2
	CGNL1	NM_001252335.2		c.2403+13892G>T		intron	N/A	NP_001239264.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CGNL1	ENST00000281282.6	TSL:1 MANE Select	c.2403+13892G>T		intron	N/A	ENSP00000281282.5
	CGNL1	ENST00000955758.1		c.2403+13892G>T		intron	N/A	ENSP00000625817.1
	CGNL1	ENST00000860577.1		c.2403+13892G>T		intron	N/A	ENSP00000530636.1

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122509 AN: 151738 Hom.: 49675 Cov.: 29

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.807 AC: 122591 AN: 151856 Hom.: 49703 Cov.: 29 AF XY: 0.807 AC XY: 59912 AN XY: 74218

African (AFR) AF: 0.765 AC: 31605 AN: 41338

American (AMR) AF: 0.823 AC: 12555 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2730 AN: 3470

East Asian (EAS) AF: 0.693 AC: 3559 AN: 5138

South Asian (SAS) AF: 0.717 AC: 3439 AN: 4796

European-Finnish (FIN) AF: 0.901 AC: 9517 AN: 10568

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56472 AN: 67982

Other (OTH) AF: 0.802 AC: 1688 AN: 2106

Alfa AF: 0.821 Hom.: 84468

Bravo AF: 0.801

Asia WGS AF: 0.671 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.21
DANN	Benign	0.49
PhyloP100		-2.2
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: rs2922219; hg19: chr15-57767982;