Variant 7-30912229-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_198098.4(AQP1):c.320T>G(p.Val107Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00332 in 1,609,408 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V107I) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0025 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0034 ( 15 hom. )

Consequence

AQP1
NM_198098.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.13

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.014616966).

BP6

Variant 7-30912229-T-G is Benign according to our data. Variant chr7-30912229-T-G is described in ClinVar as [Benign]. Clinvar id is 1589116.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 BG gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AQP1	NM_198098.4 linkuse as main transcript	c.320T>G	p.Val107Gly	missense_variant	1/4	ENST00000311813.11
AQP1	NM_001329872.2 linkuse as main transcript	c.320T>G	p.Val107Gly	missense_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP1	ENST00000311813.11 linkuse as main transcript	c.320T>G	p.Val107Gly	missense_variant	1/4	1	NM_198098.4	P1	P29972-1
AQP1	ENST00000441328.7 linkuse as main transcript	n.175T>G		non_coding_transcript_exon_variant	1/2	1
AQP1	ENST00000652696.1 linkuse as main transcript	c.320T>G	p.Val107Gly	missense_variant	1/5			P1	P29972-1
AQP1	ENST00000652692.1 linkuse as main transcript	c.110T>G	p.Val37Gly	missense_variant	1/5

Frequencies

GnomAD3 genomes

AF:

0.00254

AC:

386

AN:

152134

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000604

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.00223

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00264

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00412

Gnomad OTH

AF:

0.000958

GnomAD3 exomes

AF:

0.00239

AC:

590

AN:

247376

Hom.:

AF XY:

0.00241

AC XY:

323

AN XY:

134124

show subpopulations

Gnomad AFR exome

AF:

0.000432

Gnomad AMR exome

AF:

0.00122

Gnomad ASJ exome

AF:

0.0000994

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000980

Gnomad FIN exome

AF:

0.00378

Gnomad NFE exome

AF:

0.00374

Gnomad OTH exome

AF:

0.00263

GnomAD4 exome

AF:

0.00340

AC:

4951

AN:

1457156

Hom.:

Cov.:

AF XY:

0.00328

AC XY:

2381

AN XY:

725162

show subpopulations

Gnomad4 AFR exome

AF:

0.000538

Gnomad4 AMR exome

AF:

0.00121

Gnomad4 ASJ exome

AF:

0.0000765

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000788

Gnomad4 FIN exome

AF:

0.00326

Gnomad4 NFE exome

AF:

0.00402

Gnomad4 OTH exome

AF:

0.00292

GnomAD4 genome

AF:

0.00254

AC:

386

AN:

152252

Hom.:

Cov.:

AF XY:

0.00259

AC XY:

193

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.000602

Gnomad4 AMR

AF:

0.00222

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00264

Gnomad4 NFE

AF:

0.00412

Gnomad4 OTH

AF:

0.000948

Alfa

AF:

0.00302

Hom.:

Bravo

AF:

0.00241

TwinsUK

AF:

0.00324

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00198

AC:

ExAC

AF:

0.00254

AC:

309

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00294

EpiControl

AF:

0.00267

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

Invitae

Nov 27, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.39

BayesDel_addAF

Benign

-0.10

BayesDel_noAF

Uncertain

0.080

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Pathogenic

0.80

Eigen

Pathogenic

0.69

Eigen_PC

Uncertain

0.62

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.75

M_CAP

Uncertain

0.22

MetaRNN

Benign

0.015

MetaSVM

Uncertain

0.69

MutationAssessor

Benign

2.0

MutationTaster

Benign

1.0

D;D

PROVEAN

Uncertain

-2.4

REVEL

Pathogenic

0.84

Sift

Uncertain

0.0020

Sift4G

Benign

0.17

Polyphen

1.0

Vest4

0.49

MVP

0.94

MPC

1.4

ClinPred

0.037

GERP RS

4.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.77

gMVP

0.90

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