dbSNP rs10270308: CDHR3:p.Asp778Asp (chr7-106030821-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_152750.5(CDHR3):c.2334T>C(p.Asp778Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 1,610,650 control chromosomes in the GnomAD database, including 8,048 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 0.12 ( 2747 hom., cov: 33)

Exomes 𝑓: 0.031 ( 5301 hom. )

Consequence

CDHR3
NM_152750.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.529

Publications

14 publications found

Variant links:

Genes affected

CDHR3 (HGNC:26308): (cadherin related family member 3) Predicted to enable cadherin binding activity and calcium ion binding activity. Predicted to be involved in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; cell morphogenesis; and cell-cell junction organization. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

CDHR3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP7

Synonymous conserved (PhyloP=0.529 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDHR3	NM_152750.5 link	c.2334T>C	p.Asp778Asp	synonymous_variant	Exon 18 of 19	ENST00000317716.14	NP_689963.2	Q6ZTQ4-1
CDHR3	NM_001301161.2 link	c.2070T>C	p.Asp690Asp	synonymous_variant	Exon 17 of 18		NP_001288090.1	Q6ZTQ4E7EQG5B7Z8X2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR3	ENST00000317716.14 link	c.2334T>C	p.Asp778Asp	synonymous_variant	Exon 18 of 19	1	NM_152750.5	ENSP00000325954.9		Q6ZTQ4-1

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18282

AN:

152124

Hom.:

2738

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.380

Gnomad SAS

AF:

0.0727

Gnomad FIN

AF:

0.0271

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.00570

Gnomad OTH

AF:

0.110

GnomAD2 exomes

AF:

0.0770

AC:

18760

AN:

243556

AF XY:

0.0667

show subpopulations

Gnomad AFR exome

AF:

0.330

Gnomad AMR exome

AF:

0.129

Gnomad ASJ exome

AF:

0.00151

Gnomad EAS exome

AF:

0.371

Gnomad FIN exome

AF:

0.0273

Gnomad NFE exome

AF:

0.00601

Gnomad OTH exome

AF:

0.0464

GnomAD4 exome

AF:

0.0312

AC:

45455

AN:

1458406

Hom.:

5301

Cov.:

AF XY:

0.0303

AC XY:

21936

AN XY:

725106

show subpopulations

African (AFR)

AF:

0.340

AC:

11348

AN:

33364

American (AMR)

AF:

0.128

AC:

5639

AN:

44208

Ashkenazi Jewish (ASJ)

AF:

0.00119

AC:

AN:

26034

East Asian (EAS)

AF:

0.352

AC:

13911

AN:

39532

South Asian (SAS)

AF:

0.0515

AC:

4388

AN:

85266

European-Finnish (FIN)

AF:

0.0258

AC:

1375

AN:

53236

Middle Eastern (MID)

AF:

0.0321

AC:

185

AN:

5762

European-Non Finnish (NFE)

AF:

0.00455

AC:

5054

AN:

1110768

Other (OTH)

AF:

0.0585

AC:

3524

AN:

60236

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.436

Heterozygous variant carriers

1602

3204

4807

6409

8011

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

716

1432

2148

2864

3580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.120

AC:

18330

AN:

152244

Hom.:

2747

Cov.:

AF XY:

0.120

AC XY:

8943

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.326

AC:

13508

AN:

41496

American (AMR)

AF:

0.101

AC:

1551

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.00115

AC:

AN:

3470

East Asian (EAS)

AF:

0.380

AC:

1970

AN:

5186

South Asian (SAS)

AF:

0.0724

AC:

349

AN:

4822

European-Finnish (FIN)

AF:

0.0271

AC:

288

AN:

10616

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00570

AC:

388

AN:

68026

Other (OTH)

AF:

0.111

AC:

235

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

654

1308

1962

2616

3270

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0480

Hom.:

4352

Bravo

AF:

0.137

Asia WGS

AF:

0.226

AC:

785

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

7.2

(source)

DANN

Benign

0.59

PhyloP100

0.53

Mutation Taster

=91/9

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over