Variant 1-154321270-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_080429.3(AQP10):c.105+10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00926 in 1,607,486 control chromosomes in the GnomAD database, including 192 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 28 hom., cov: 31)

Exomes 𝑓: 0.0092 ( 164 hom. )

Consequence

AQP10
NM_080429.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.320

Variant links:

Genes affected

AQP10 (HGNC:16029): (aquaporin 10) This gene encodes a member of the aquaglyceroporin family of integral membrane proteins. Members of this family function as water-permeable channels in the epithelia of organs that absorb and excrete water. This protein was shown to function as a water-selective channel, and could also permeate neutral solutes such as glycerol and urea. [provided by RefSeq, Jul 2008]

AQP10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 1-154321270-A-G is Benign according to our data. Variant chr1-154321270-A-G is described in ClinVar as [Benign]. Clinvar id is 777751.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 28 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
AQP10	NM_080429.3 link	c.105+10A>G	intron_variant	Intron 1 of 5	ENST00000324978.8	NP_536354.2	Q96PS8-1
AQP10	XM_011510104.3 link	c.105+10A>G	intron_variant	Intron 1 of 5		XP_011508406.1
AQP10	XM_047433547.1 link	c.-33+10A>G	intron_variant	Intron 1 of 4		XP_047289503.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
AQP10	ENST00000324978.8 link	c.105+10A>G	intron_variant	Intron 1 of 5	1	NM_080429.3	ENSP00000318355.3	Q96PS8-1
AQP10	ENST00000484864.1 link	c.105+10A>G	intron_variant	Intron 1 of 4	1		ENSP00000420341.1	Q96PS8-2
AQP10	ENST00000355197.4 link	n.171+10A>G	intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.0101

AC:

1536

AN:

152016

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000870

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00347

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00479

Gnomad FIN

AF:

0.0318

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0155

Gnomad OTH

AF:

0.00766

GnomAD3 exomes

AF:

0.00878

AC:

2150

AN:

244944

Hom.:

AF XY:

0.00863

AC XY:

1146

AN XY:

132754

show subpopulations

Gnomad AFR exome

AF:

0.000697

Gnomad AMR exome

AF:

0.00216

Gnomad ASJ exome

AF:

0.00667

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00338

Gnomad FIN exome

AF:

0.0306

Gnomad NFE exome

AF:

0.0109

Gnomad OTH exome

AF:

0.00774

GnomAD4 exome

AF:

0.00917

AC:

13347

AN:

1455352

Hom.:

164

Cov.:

AF XY:

0.00939

AC XY:

6797

AN XY:

724128

show subpopulations

Gnomad4 AFR exome

AF:

0.000848

Gnomad4 AMR exome

AF:

0.00229

Gnomad4 ASJ exome

AF:

0.00785

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00309

Gnomad4 FIN exome

AF:

0.0324

Gnomad4 NFE exome

AF:

0.00946

Gnomad4 OTH exome

AF:

0.00900

GnomAD4 genome

AF:

0.0101

AC:

1535

AN:

152134

Hom.:

Cov.:

AF XY:

0.0105

AC XY:

782

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.000867

Gnomad4 AMR

AF:

0.00347

Gnomad4 ASJ

AF:

0.00519

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00458

Gnomad4 FIN

AF:

0.0318

Gnomad4 NFE

AF:

0.0155

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.0187

Hom.:

Bravo

AF:

0.00579

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Dec 14, 2017

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.9

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

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