Variant 5-31317387-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_004932.4(CDH6):c.1525C>T(p.Leu509Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 1,538,908 control chromosomes in the GnomAD database, including 216,835 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 0.50 ( 19833 hom., cov: 32)

Exomes 𝑓: 0.53 ( 197002 hom. )

Consequence

CDH6
NM_004932.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.717

Variant links:

Genes affected

CDH6 (HGNC:1765): (cadherin 6) This gene encodes a member of the cadherin superfamily. Cadherins are membrane glycoproteins that mediate homophilic cell-cell adhesion and play critical roles in cell differentiation and morphogenesis. The encoded protein is a type II cadherin and may play a role in kidney development as well as endometrium and placenta formation. Decreased expression of this gene may be associated with tumor growth and metastasis. [provided by RefSeq, May 2011]

CDH6 links:

CDH6 (HGNC:):

CDH6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDH6	NM_004932.4 linkuse as main transcript	c.1525C>T	p.Leu509Leu	synonymous_variant	10/12	ENST00000265071.3	NP_004923.1	P55285-1
CDH6	NM_001362435.2 linkuse as main transcript	c.1525C>T	p.Leu509Leu	synonymous_variant	10/11		NP_001349364.1
CDH6	XM_011513921.4 linkuse as main transcript	c.1525C>T	p.Leu509Leu	synonymous_variant	10/12		XP_011512223.1	P55285-1
CDH6	XM_047416591.1 linkuse as main transcript	c.1525C>T	p.Leu509Leu	synonymous_variant	10/12		XP_047272547.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CDH6	ENST00000265071.3 linkuse as main transcript	c.1525C>T	p.Leu509Leu	synonymous_variant	10/12	2	NM_004932.4	ENSP00000265071.2	P55285-1
CDH6	ENST00000514738.5 linkuse as main transcript	c.1360C>T	p.Leu454Leu	synonymous_variant	10/11	1		ENSP00000424843.1	D6RF86
CDH6	ENST00000504835.1 linkuse as main transcript	n.93C>T		non_coding_transcript_exon_variant	2/3	5

Frequencies

GnomAD3 genomes

AF:

0.503

AC:

76448

AN:

151926

Hom.:

19812

Cov.:

show subpopulations

Gnomad AFR

AF:

0.383

Gnomad AMI

AF:

0.436

Gnomad AMR

AF:

0.525

Gnomad ASJ

AF:

0.550

Gnomad EAS

AF:

0.523

Gnomad SAS

AF:

0.481

Gnomad FIN

AF:

0.654

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.548

Gnomad OTH

AF:

0.480

GnomAD3 exomes

AF:

0.532

AC:

128561

AN:

241780

Hom.:

34685

AF XY:

0.533

AC XY:

69608

AN XY:

130560

show subpopulations

Gnomad AFR exome

AF:

0.383

Gnomad AMR exome

AF:

0.522

Gnomad ASJ exome

AF:

0.539

Gnomad EAS exome

AF:

0.521

Gnomad SAS exome

AF:

0.499

Gnomad FIN exome

AF:

0.660

Gnomad NFE exome

AF:

0.541

Gnomad OTH exome

AF:

0.525

GnomAD4 exome

AF:

0.528

AC:

732308

AN:

1386864

Hom.:

197002

Cov.:

AF XY:

0.529

AC XY:

366250

AN XY:

692710

show subpopulations

Gnomad4 AFR exome

AF:

0.368

Gnomad4 AMR exome

AF:

0.522

Gnomad4 ASJ exome

AF:

0.540

Gnomad4 EAS exome

AF:

0.546

Gnomad4 SAS exome

AF:

0.509

Gnomad4 FIN exome

AF:

0.655

Gnomad4 NFE exome

AF:

0.528

Gnomad4 OTH exome

AF:

0.521

GnomAD4 genome

AF:

0.503

AC:

76509

AN:

152044

Hom.:

19833

Cov.:

AF XY:

0.509

AC XY:

37833

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.383

Gnomad4 AMR

AF:

0.526

Gnomad4 ASJ

AF:

0.550

Gnomad4 EAS

AF:

0.524

Gnomad4 SAS

AF:

0.481

Gnomad4 FIN

AF:

0.654

Gnomad4 NFE

AF:

0.548

Gnomad4 OTH

AF:

0.479

Alfa

AF:

0.530

Hom.:

34805

Bravo

AF:

0.489

Asia WGS

AF:

0.454

AC:

1575

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

DANN

Benign

0.75

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over