Genetic Variant AQP1:n.522G>A (chr7-30924207-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_198098.4(AQP1):c.*578G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

AQP1
NM_198098.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.337

Publications

28 publications found

Variant links:

Genes affected

AQP1 (HGNC:633): (aquaporin 1 (Colton blood group)) This gene encodes a small integral membrane protein with six bilayer spanning domains that functions as a water channel protein. This protein permits passive transport of water along an osmotic gradient. This gene is a possible candidate for disorders involving imbalance in ocular fluid movement. [provided by RefSeq, Aug 2016]

AQP1 Gene-Disease associations (from GenCC):

pulmonary arterial hypertension
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics, ClinGen

AQP1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AQP1	NM_198098.4 link	c.*578G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000311813.11	NP_932766.1	P29972-1A0A024RA31
AQP1	NM_001329872.2 link	c.*198G>A		3_prime_UTR_variant	Exon 5 of 5		NP_001316801.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AQP1	ENST00000311813.11 link	c.*578G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_198098.4	ENSP00000311165.4		P29972-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

790104

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

377662

African (AFR)

AF:

0.00

AC:

AN:

16686

American (AMR)

AF:

0.00

AC:

AN:

8806

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

7608

East Asian (EAS)

AF:

0.00

AC:

AN:

11186

South Asian (SAS)

AF:

0.00

AC:

AN:

34686

European-Finnish (FIN)

AF:

0.00

AC:

AN:

8638

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1750

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

672132

Other (OTH)

AF:

0.00

AC:

AN:

28612

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.0

(source)

DANN

Benign

0.93

PhyloP100

-0.34

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over