Variant rs6685323 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_080429.3(AQP10):c.367C>T(p.His123Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,613,838 control chromosomes in the GnomAD database, including 76,311 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.30 ( 6928 hom., cov: 32)

Exomes 𝑓: 0.31 ( 69383 hom. )

Consequence

AQP10
NM_080429.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0029536784).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
AQP10	NM_080429.3 linkuse as main transcript	c.367C>T	p.His123Tyr	missense_variant	3/6	ENST00000324978.8	NP_536354.2
AQP10	XM_011510104.3 linkuse as main transcript	c.370C>T	p.His124Tyr	missense_variant	3/6		XP_011508406.1
AQP10	XM_047433547.1 linkuse as main transcript	c.103C>T	p.His35Tyr	missense_variant	2/5		XP_047289503.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AQP10	ENST00000324978.8 linkuse as main transcript	c.367C>T	p.His123Tyr	missense_variant	3/6	1	NM_080429.3	ENSP00000318355	P1	Q96PS8-1
AQP10	ENST00000484864.1 linkuse as main transcript	c.367C>T	p.His123Tyr	missense_variant	3/5	1		ENSP00000420341		Q96PS8-2
AQP10	ENST00000355197.4 linkuse as main transcript	n.306C>T		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

45717

AN:

151882

Hom.:

6919

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.354

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.372

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.287

GnomAD3 exomes

AF:

0.292

AC:

73523

AN:

251454

Hom.:

11190

AF XY:

0.299

AC XY:

40660

AN XY:

135896

show subpopulations

Gnomad AFR exome

AF:

0.314

Gnomad AMR exome

AF:

0.215

Gnomad ASJ exome

AF:

0.209

Gnomad EAS exome

AF:

0.227

Gnomad SAS exome

AF:

0.345

Gnomad FIN exome

AF:

0.367

Gnomad NFE exome

AF:

0.303

Gnomad OTH exome

AF:

0.287

GnomAD4 exome

AF:

0.306

AC:

446718

AN:

1461838

Hom.:

69383

Cov.:

AF XY:

0.307

AC XY:

223560

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.316

Gnomad4 AMR exome

AF:

0.216

Gnomad4 ASJ exome

AF:

0.212

Gnomad4 EAS exome

AF:

0.228

Gnomad4 SAS exome

AF:

0.346

Gnomad4 FIN exome

AF:

0.361

Gnomad4 NFE exome

AF:

0.309

Gnomad4 OTH exome

AF:

0.300

GnomAD4 genome

AF:

0.301

AC:

45761

AN:

152000

Hom.:

6928

Cov.:

AF XY:

0.304

AC XY:

22552

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.247

Gnomad4 ASJ

AF:

0.205

Gnomad4 EAS

AF:

0.223

Gnomad4 SAS

AF:

0.326

Gnomad4 FIN

AF:

0.372

Gnomad4 NFE

AF:

0.305

Gnomad4 OTH

AF:

0.292

Alfa

AF:

0.295

Hom.:

8866

Bravo

AF:

0.289

TwinsUK

AF:

0.288

AC:

1067

ALSPAC

AF:

0.299

AC:

1152

ESP6500AA

AF:

0.308

AC:

1358

ESP6500EA

AF:

0.296

AC:

2542

ExAC

AF:

0.297

AC:

36076

Asia WGS

AF:

0.272

AC:

944

AN:

3478

EpiCase

AF:

0.299

EpiControl

AF:

0.299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.072

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Benign

2.6

DANN

Benign

0.48

DEOGEN2

Benign

0.071

T;.

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.78

FATHMM_MKL

Benign

0.52

LIST_S2

Benign

0.16

T;T

MetaRNN

Benign

0.0030

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.99

N;N

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.42

PROVEAN

Benign

3.7

N;N

REVEL

Benign

0.21

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.066

MPC

0.85

ClinPred

0.0018

GERP RS

3.8

Varity_R

0.16

gMVP

0.65

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over