Variant 22-50484788-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001253845.2(ADM2):c.*1885T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,026 control chromosomes in the GnomAD database, including 39,547 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 0.72 ( 39522 hom., cov: 32)

Exomes 𝑓: 0.61 ( 25 hom. )

Consequence

ADM2
NM_001253845.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

Variant links:

Genes affected

ADM2 (HGNC:28898): (adrenomedullin 2) This gene encodes a member of the calcitonin gene-related peptide (CGRP)/calcitonin family of hormones that play a role in the regulation of cardiovascular homeostasis, prolactin release, anti-diuresis, anti-natriuresis, and regulation of food and water intake. The encoded protein is proteolytically processed to generate one or more biologically active peptides. [provided by RefSeq, Jul 2015]

ADM2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADM2	NM_001253845.2 link	c.*1885T>C		3_prime_UTR_variant	3/3	ENST00000395737.2	NP_001240774.1	Q7Z4H4
ADM2	NM_001369882.1 link	c.*1885T>C		3_prime_UTR_variant	2/2		NP_001356811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADM2	ENST00000395737.2 link	c.*1885T>C		3_prime_UTR_variant	3/3	1	NM_001253845.2	ENSP00000379086.1		Q7Z4H4
ADM2	ENST00000395738.2 link	c.*1885T>C		3_prime_UTR_variant	2/2	1		ENSP00000379087.2		Q7Z4H4

Frequencies

GnomAD3 genomes

AF:

0.716

AC:

108681

AN:

151786

Hom.:

39481

Cov.:

show subpopulations

Gnomad AFR

AF:

0.813

Gnomad AMI

AF:

0.813

Gnomad AMR

AF:

0.668

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.912

Gnomad SAS

AF:

0.716

Gnomad FIN

AF:

0.764

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.657

Gnomad OTH

AF:

0.669

GnomAD4 exome

AF:

0.607

AC:

AN:

122

Hom.:

Cov.:

AF XY:

0.659

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.631

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.716

AC:

108778

AN:

151904

Hom.:

39522

Cov.:

AF XY:

0.720

AC XY:

53484

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.813

Gnomad4 AMR

AF:

0.667

Gnomad4 ASJ

AF:

0.520

Gnomad4 EAS

AF:

0.912

Gnomad4 SAS

AF:

0.716

Gnomad4 FIN

AF:

0.764

Gnomad4 NFE

AF:

0.657

Gnomad4 OTH

AF:

0.672

Alfa

AF:

0.651

Hom.:

28633

Bravo

AF:

0.716

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.7

DANN

Benign

0.27

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