15-57470595-C-T

Variant names:

• chr15-57470595-C-T
• rs2934442
• NM_032866.5:c.2403+8703C>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+8703C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,210 control chromosomes in the GnomAD database, including 54,618 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 0.84 (54618 hom., cov: 32)
• Consequence: CGNL1 NM_032866.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CGNL1	NM_032866.5	c.2403+8703C>T		intron_variant	Intron 8 of 18	ENST00000281282.6	NP_116255.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CGNL1	ENST00000281282.6	c.2403+8703C>T		intron_variant	Intron 8 of 18	1	NM_032866.5	ENSP00000281282.5

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128493 AN: 152092 Hom.: 54558 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.845 AC: 128613 AN: 152210 Hom.: 54618 Cov.: 32 AF XY: 0.849 AC XY: 63183 AN XY: 74412

African (AFR) AF: 0.925 AC: 38407 AN: 41536

American (AMR) AF: 0.833 AC: 12744 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2641 AN: 3472

East Asian (EAS) AF: 0.922 AC: 4773 AN: 5178

South Asian (SAS) AF: 0.890 AC: 4286 AN: 4816

European-Finnish (FIN) AF: 0.868 AC: 9197 AN: 10596

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53965 AN: 68010

Other (OTH) AF: 0.827 AC: 1742 AN: 2106

Alfa AF: 0.807 Hom.: 213804

Bravo AF: 0.842

Asia WGS AF: 0.894 AC: 3108 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.74
DANN	Benign	0.11
PhyloP100		-0.74
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: rs2934442; hg19: chr15-57762793;