dbSNP rs34354539: ADM:c.*563dupC (chr11-10307200-T-TC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001124.3(ADM):c.*563dupC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.48 ( 18286 hom., cov: 0)

Exomes 𝑓: 0.52 ( 59 hom. )

Consequence

ADM
NM_001124.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.163

Publications

4 publications found

Variant links:

Genes affected

ADM (HGNC:259): (adrenomedullin) The protein encoded by this gene is a preprohormone which is cleaved to form two biologically active peptides, adrenomedullin and proadrenomedullin N-terminal 20 peptide. Adrenomedullin is a 52 aa peptide with several functions, including vasodilation, regulation of hormone secretion, promotion of angiogenesis, and antimicrobial activity. The antimicrobial activity is antibacterial, as the peptide has been shown to kill E. coli and S. aureus at low concentration. [provided by RefSeq, Aug 2014]

ADM links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADM	NM_001124.3 link	c.*563dupC		3_prime_UTR_variant	Exon 4 of 4	ENST00000278175.10	NP_001115.1	P35318

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ADM	ENST00000278175.10 link	c.*563dupC	3_prime_UTR_variant	Exon 4 of 4	1	NM_001124.3	ENSP00000278175.5	P35318
ADM	ENST00000528655.5 link	c.*563dupC	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000436607.1	P35318
ADM	ENST00000534464.1 link	c.*563dupC	3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000431438.1	E9PL83
ADM	ENST00000530439.1 link	c.*563dupC	3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000436837.1	E9PQE6

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

73459

AN:

151904

Hom.:

18255

Cov.:

show subpopulations

Gnomad AFR

AF:

0.380

Gnomad AMI

AF:

0.441

Gnomad AMR

AF:

0.487

Gnomad ASJ

AF:

0.524

Gnomad EAS

AF:

0.328

Gnomad SAS

AF:

0.487

Gnomad FIN

AF:

0.557

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.545

Gnomad OTH

AF:

0.482

GnomAD4 exome

AF:

0.523

AC:

231

AN:

442

Hom.:

Cov.:

AF XY:

0.522

AC XY:

141

AN XY:

270

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.525

AC:

227

AN:

432

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.484

AC:

73553

AN:

152022

Hom.:

18286

Cov.:

AF XY:

0.485

AC XY:

36038

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.380

AC:

15768

AN:

41442

American (AMR)

AF:

0.488

AC:

7456

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.524

AC:

1818

AN:

3468

East Asian (EAS)

AF:

0.329

AC:

1698

AN:

5164

South Asian (SAS)

AF:

0.486

AC:

2342

AN:

4814

European-Finnish (FIN)

AF:

0.557

AC:

5885

AN:

10560

Middle Eastern (MID)

AF:

0.490

AC:

144

AN:

294

European-Non Finnish (NFE)

AF:

0.545

AC:

37021

AN:

67978

Other (OTH)

AF:

0.483

AC:

1019

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1909

3818

5726

7635

9544

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.508

Hom.:

2456

Bravo

AF:

0.466

Asia WGS

AF:

0.373

AC:

1297

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.16

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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rs34354539

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