11-77590427-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_173039.3(AQP11):c.435G>T(p.Gln145His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00576 in 1,614,088 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q145P) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0043 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0059 (37 hom.)
• Consequence: AQP11 NM_173039.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.305

Genes affected

AQP11 (HGNC:19940): (aquaporin 11) Enables glycerol channel activity and water channel activity. Involved in several processes, including glycerol transport; hydrogen peroxide transmembrane transport; and protein homooligomerization. Located in cell surface; endoplasmic reticulum; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

CLNS1A (HGNC:2080): (chloride nucleotide-sensitive channel 1A) This gene encodes a protein that functions in multiple regulatory pathways. The encoded protein complexes with numerous cytosolic proteins and performs diverse functions including regulation of small nuclear ribonucleoprotein biosynthesis, platelet activation and cytoskeletal organization. The protein is also found associated with the plasma membrane where it functions as a chloride current regulator. Pseudogenes of this gene are found on chromosomes 1, 4 and 6. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0056094825).
• BP6: Variant 11-77590427-G-T is Benign according to our data. Variant chr11-77590427-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2642191.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AQP11	NM_173039.3	c.435G>T	p.Gln145His	missense_variant	1/3	ENST00000313578.4
AQP11	NM_001363477.2	c.435G>T	p.Gln145His	missense_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP11	ENST00000313578.4	c.435G>T	p.Gln145His	missense_variant	1/3	1	NM_173039.3	P1
AQP11	ENST00000528638.1	n.291-102G>T		intron_variant, non_coding_transcript_variant		1
CLNS1A	ENST00000526761.5	c.*156-4968C>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.00433 AC: 659 AN: 152130 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00174

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00890

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000623

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00622

Gnomad OTH AF: 0.00670

GnomAD3 exomes AF: 0.00395 AC: 993 AN: 251434 Hom.: 5 AF XY: 0.00406 AC XY: 552 AN XY: 135922

Gnomad AFR exome AF: 0.00105

Gnomad AMR exome AF: 0.00494

Gnomad ASJ exome AF: 0.00218

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00144

Gnomad FIN exome AF: 0.000370

Gnomad NFE exome AF: 0.00613

Gnomad OTH exome AF: 0.00538

GnomAD4 exome AF: 0.00591 AC: 8641 AN: 1461840 Hom.: 37 Cov.: 33 AF XY: 0.00582 AC XY: 4229 AN XY: 727232

Gnomad4 AFR exome AF: 0.00119

Gnomad4 AMR exome AF: 0.00530

Gnomad4 ASJ exome AF: 0.00253

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.00134

Gnomad4 FIN exome AF: 0.000337

Gnomad4 NFE exome AF: 0.00696

Gnomad4 OTH exome AF: 0.00621

GnomAD4 genome AF: 0.00432 AC: 658 AN: 152248 Hom.: 3 Cov.: 32 AF XY: 0.00414 AC XY: 308 AN XY: 74438

Gnomad4 AFR AF: 0.00173

Gnomad4 AMR AF: 0.00889

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000623

Gnomad4 FIN AF: 0.0000943

Gnomad4 NFE AF: 0.00622

Gnomad4 OTH AF: 0.00663

Alfa AF: 0.00613 Hom.: 9

Bravo AF: 0.00461

TwinsUK AF: 0.00647 AC: 24

ALSPAC AF: 0.00545 AC: 21

ESP6500AA AF: 0.00205 AC: 9

ESP6500EA AF: 0.00524 AC: 45

ExAC AF: 0.00368 AC: 447

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00883

EpiControl AF: 0.00688

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

AQP11: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.48	T
BayesDel_noAF	Benign	-0.45
Cadd	Benign	17
Dann	Benign	0.95
DEOGEN2	Benign	0.38	T
Eigen	Benign	-0.92
Eigen_PC	Benign	-0.81
FATHMM_MKL	Benign	0.30	N
LIST_S2	Benign	0.45	T
M_CAP	Uncertain	0.086	D
MetaRNN	Benign	0.0056	T
MetaSVM	Benign	-0.85	T
MutationAssessor	Benign	1.2	L
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-1.4	N
REVEL	Benign	0.093
Sift	Benign	0.067	T
Sift4G	Uncertain	0.042	D
Polyphen		0.0	B
Vest4		0.021
MutPred		0.38		Gain of catalytic residue at Q145 (P = 0.06);
MVP		0.79
MPC		0.83
ClinPred		0.0059	T
GERP RS		2.5
Varity_R		0.064
gMVP		0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs117458417; hg19: chr11-77301472; COSMIC: COSV99047013;