dbSNP rs3758650: CDHR5:c.*486C>T (chr11-616865-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021924.5(CDHR5):c.*486C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0494 in 179,030 control chromosomes in the GnomAD database, including 321 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 0.048 ( 256 hom., cov: 33)

Exomes 𝑓: 0.057 ( 65 hom. )

Consequence

CDHR5
NM_021924.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.693

Publications

25 publications found

Variant links:

Genes affected

CDHR5 (HGNC:7521): (cadherin related family member 5) This gene is a novel mucin-like gene that is a member of the cadherin superfamily. While encoding nonpolymorphic tandem repeats rich in proline, serine and threonine similar to mucin proteins, the gene also contains sequence encoding calcium-binding motifs found in all cadherins. The role of the hybrid extracellular region and the specific function of this protein have not yet been determined. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jan 2010]

CDHR5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDHR5	NM_021924.5 link	c.*486C>T		3_prime_UTR_variant	Exon 15 of 15	ENST00000397542.7	NP_068743.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR5	ENST00000397542.7 link	c.*486C>T		3_prime_UTR_variant	Exon 15 of 15	1	NM_021924.5	ENSP00000380676.2
CDHR5	ENST00000358353.8 link	c.*486C>T		3_prime_UTR_variant	Exon 15 of 15	5		ENSP00000351118.4

Frequencies

GnomAD3 genomes

AF:

0.0482

AC:

7331

AN:

152166

Hom.:

258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0171

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.0271

Gnomad ASJ

AF:

0.0423

Gnomad EAS

AF:

0.0921

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.0929

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0572

Gnomad OTH

AF:

0.0396

GnomAD2 exomes

AF:

0.0576

AC:

765

AN:

13282

AF XY:

0.0576

show subpopulations

Gnomad AFR exome

AF:

0.00718

Gnomad AMR exome

AF:

0.0217

Gnomad ASJ exome

AF:

0.0542

Gnomad EAS exome

AF:

0.0824

Gnomad FIN exome

AF:

0.0946

Gnomad NFE exome

AF:

0.0548

Gnomad OTH exome

AF:

0.0430

GnomAD4 exome

AF:

0.0569

AC:

1522

AN:

26746

Hom.:

Cov.:

AF XY:

0.0607

AC XY:

885

AN XY:

14574

show subpopulations

African (AFR)

AF:

0.0213

AC:

AN:

328

American (AMR)

AF:

0.0151

AC:

AN:

1192

Ashkenazi Jewish (ASJ)

AF:

0.0402

AC:

AN:

572

East Asian (EAS)

AF:

0.0717

AC:

AN:

586

South Asian (SAS)

AF:

0.0883

AC:

399

AN:

4518

European-Finnish (FIN)

AF:

0.0811

AC:

115

AN:

1418

Middle Eastern (MID)

AF:

0.0419

AC:

AN:

1720

European-Non Finnish (NFE)

AF:

0.0514

AC:

763

AN:

14856

Other (OTH)

AF:

0.0533

AC:

AN:

1556

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

130

196

261

326

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0481

AC:

7328

AN:

152284

Hom.:

256

Cov.:

AF XY:

0.0512

AC XY:

3814

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.0171

AC:

710

AN:

41580

American (AMR)

AF:

0.0269

AC:

412

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0423

AC:

147

AN:

3472

East Asian (EAS)

AF:

0.0923

AC:

477

AN:

5168

South Asian (SAS)

AF:

0.111

AC:

538

AN:

4834

European-Finnish (FIN)

AF:

0.0929

AC:

985

AN:

10606

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0572

AC:

3889

AN:

67996

Other (OTH)

AF:

0.0388

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

360

719

1079

1438

1798

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0506

Hom.:

489

Bravo

AF:

0.0404

Asia WGS

AF:

0.0800

AC:

279

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.59

(source)

DANN

Benign

0.77

PhyloP100

-0.69

Mutation Taster

=100/0

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