NM_001651.4:c.363+19_363+21dupGGG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001651.4(AQP5):​c.363+19_363+21dupGGG variant causes a intron 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 0.000033 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000029 ( 0 hom. )

Consequence

AQP5
NM_001651.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.227
Variant links:
Genes affected
AQP5 (HGNC:638): (aquaporin 5) Aquaporin 5 (AQP5) is a water channel protein. Aquaporins are a family of small integral membrane proteins related to the major intrinsic protein (MIP or AQP0). Aquaporin 5 plays a role in the generation of saliva, tears and pulmonary secretions. AQP0, AQP2, AQP5, and AQP6 are closely related and all map to 12q13. [provided by RefSeq, Jul 2008]
AQP5-AS1 (HGNC:55474): (AQP5 and AQP2 antisense RNA 2)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 5 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AQP5NM_001651.4 linkc.363+19_363+21dupGGG intron_variant Intron 1 of 3 ENST00000293599.7 NP_001642.1 P55064

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AQP5ENST00000293599.7 linkc.363+11_363+12insGGG intron_variant Intron 1 of 3 1 NM_001651.4 ENSP00000293599.5 P55064
AQP5-AS1ENST00000550214.1 linkn.258+275_258+276insCCC intron_variant Intron 1 of 1 2
AQP5-AS1ENST00000550530.1 linkn.117+275_117+276insCCC intron_variant Intron 1 of 2 3
AQP5-AS1ENST00000552379.1 linkn.256+275_256+276insCCC intron_variant Intron 1 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.0000334
AC:
5
AN:
149906
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000126
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000288
AC:
4
AN:
1387220
Hom.:
0
Cov.:
0
AF XY:
0.00000292
AC XY:
2
AN XY:
685954
show subpopulations
Gnomad4 AFR exome
AF:
0.000101
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000274
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000334
AC:
5
AN:
149906
Hom.:
0
Cov.:
0
AF XY:
0.0000547
AC XY:
4
AN XY:
73174
show subpopulations
Gnomad4 AFR
AF:
0.000126
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs3832811; hg19: chr12-50356174; API