Variant 12-49962391-TGGG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001651.4(AQP5):c.363+19_363+21del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 1,537,074 control chromosomes in the GnomAD database, including 466,606 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.71 ( 38744 hom., cov: 0)

Exomes 𝑓: 0.78 ( 427862 hom. )

Consequence

AQP5
NM_001651.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

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 links:

AQP5-AS1 (HGNC:55474): (AQP5 and AQP2 antisense RNA 2)

AQP5-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 12-49962391-TGGG-T is Benign according to our data. Variant chr12-49962391-TGGG-T is described in ClinVar as [Benign]. Clinvar id is 1283355.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AQP5	NM_001651.4 linkuse as main transcript	c.363+19_363+21del		intron_variant		ENST00000293599.7	NP_001642.1
AQP5-AS1	NR_110591.1 linkuse as main transcript	n.117+273_117+275del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
AQP5	ENST00000293599.7 linkuse as main transcript	c.363+19_363+21del	intron_variant	1	NM_001651.4	ENSP00000293599	P1
AQP5-AS1	ENST00000550530.1 linkuse as main transcript	n.117+273_117+275del	intron_variant, non_coding_transcript_variant	3
AQP5-AS1	ENST00000550214.1 linkuse as main transcript	n.258+273_258+275del	intron_variant, non_coding_transcript_variant	2
AQP5-AS1	ENST00000552379.1 linkuse as main transcript	n.256+273_256+275del	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.707

AC:

105938

AN:

149896

Hom.:

38704

Cov.:

show subpopulations

Gnomad AFR

AF:

0.511

Gnomad AMI

AF:

0.798

Gnomad AMR

AF:

0.800

Gnomad ASJ

AF:

0.718

Gnomad EAS

AF:

0.491

Gnomad SAS

AF:

0.638

Gnomad FIN

AF:

0.817

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.802

Gnomad OTH

AF:

0.708

GnomAD3 exomes

AF:

0.772

AC:

131206

AN:

170032

Hom.:

50992

AF XY:

0.768

AC XY:

72707

AN XY:

94654

show subpopulations

Gnomad AFR exome

AF:

0.553

Gnomad AMR exome

AF:

0.839

Gnomad ASJ exome

AF:

0.772

Gnomad EAS exome

AF:

0.537

Gnomad SAS exome

AF:

0.685

Gnomad FIN exome

AF:

0.849

Gnomad NFE exome

AF:

0.823

Gnomad OTH exome

AF:

0.775

GnomAD4 exome

AF:

0.783

AC:

1086049

AN:

1387068

Hom.:

427862

AF XY:

0.780

AC XY:

534975

AN XY:

685860

show subpopulations

Gnomad4 AFR exome

AF:

0.515

Gnomad4 AMR exome

AF:

0.827

Gnomad4 ASJ exome

AF:

0.738

Gnomad4 EAS exome

AF:

0.530

Gnomad4 SAS exome

AF:

0.659

Gnomad4 FIN exome

AF:

0.832

Gnomad4 NFE exome

AF:

0.808

Gnomad4 OTH exome

AF:

0.745

GnomAD4 genome

AF:

0.707

AC:

106035

AN:

150006

Hom.:

38744

Cov.:

AF XY:

0.708

AC XY:

51868

AN XY:

73284

show subpopulations

Gnomad4 AFR

AF:

0.512

Gnomad4 AMR

AF:

0.800

Gnomad4 ASJ

AF:

0.718

Gnomad4 EAS

AF:

0.490

Gnomad4 SAS

AF:

0.639

Gnomad4 FIN

AF:

0.817

Gnomad4 NFE

AF:

0.802

Gnomad4 OTH

AF:

0.712

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over