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

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001651.4(AQP5):c.363+18_363+21del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000396 in 1,537,206 control chromosomes in the GnomAD database, including 12 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00053 ( 1 hom., cov: 0)

Exomes 𝑓: 0.00038 ( 11 hom. )

Consequence

AQP5
NM_001651.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.462

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 Likely_benign. Variant got -6 ACMG points.

BP6

Variant 12-49962391-TGGGG-T is Benign according to our data. Variant chr12-49962391-TGGGG-T is described in ClinVar as [Benign]. Clinvar id is 1987458.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 80 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AQP5	NM_001651.4 linkuse as main transcript	c.363+18_363+21del		intron_variant		ENST00000293599.7	NP_001642.1
AQP5-AS1	NR_110591.1 linkuse as main transcript	n.117+272_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+18_363+21del	intron_variant	1	NM_001651.4	ENSP00000293599	P1
AQP5-AS1	ENST00000550530.1 linkuse as main transcript	n.117+272_117+275del	intron_variant, non_coding_transcript_variant	3
AQP5-AS1	ENST00000550214.1 linkuse as main transcript	n.258+272_258+275del	intron_variant, non_coding_transcript_variant	2
AQP5-AS1	ENST00000552379.1 linkuse as main transcript	n.256+272_256+275del	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.000534

AC:

AN:

149912

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000202

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00453

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000209

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.000482

GnomAD3 exomes

AF:

0.00235

AC:

400

AN:

170032

Hom.:

AF XY:

0.00175

AC XY:

166

AN XY:

94654

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0147

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000969

Gnomad FIN exome

AF:

0.000109

Gnomad NFE exome

AF:

0.0000245

Gnomad OTH exome

AF:

0.00141

GnomAD4 exome

AF:

0.000381

AC:

528

AN:

1387182

Hom.:

AF XY:

0.000324

AC XY:

222

AN XY:

685936

show subpopulations

Gnomad4 AFR exome

AF:

0.0000672

Gnomad4 AMR exome

AF:

0.0131

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000389

Gnomad4 FIN exome

AF:

0.0000529

Gnomad4 NFE exome

AF:

0.0000120

Gnomad4 OTH exome

AF:

0.000315

GnomAD4 genome

AF:

0.000533

AC:

AN:

150024

Hom.:

Cov.:

AF XY:

0.000464

AC XY:

AN XY:

73298

show subpopulations

Gnomad4 AFR

AF:

0.000201

Gnomad4 AMR

AF:

0.00452

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000210

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.000477

Alfa

AF:

0.000149

Hom.:

366

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 22, 2024

- -

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