NM_080429.3:c.20C>G

Variant names:

• chr1-154321175-C-G
• NM_080429.3:c.20C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_080429.3(AQP10):​c.20C>G​(p.Pro7Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. P7L) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: AQP10 NM_080429.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.053916216).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AQP10	NM_080429.3	c.20C>G	p.Pro7Arg	missense_variant	Exon 1 of 6	ENST00000324978.8	NP_536354.2
AQP10	XM_011510104.3	c.20C>G	p.Pro7Arg	missense_variant	Exon 1 of 6		XP_011508406.1
AQP10	XM_047433547.1	c.-118C>G		5_prime_UTR_variant	Exon 1 of 5		XP_047289503.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AQP10	ENST00000324978.8	c.20C>G	p.Pro7Arg	missense_variant	Exon 1 of 6	1	NM_080429.3	ENSP00000318355.3
AQP10	ENST00000484864.1	c.20C>G	p.Pro7Arg	missense_variant	Exon 1 of 5	1		ENSP00000420341.1
AQP10	ENST00000355197.4	n.86C>G		non_coding_transcript_exon_variant	Exon 1 of 4	5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461336 Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1 AN XY: 726980

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.092
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	0.0070
DANN	Benign	0.50
DEOGEN2	Benign	0.021	T;.
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.028	N
LIST_S2	Benign	0.26	T;T
M_CAP	Benign	0.045	D
MetaRNN	Benign	0.054	T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	-0.34	N;N
PrimateAI	Benign	0.31	T
PROVEAN	Benign	1.2	N;N
REVEL	Benign	0.15
Sift	Benign	0.73	T;T
Sift4G	Benign	0.76	T;T
Polyphen		0.0050	B;B
Vest4		0.051
MutPred		0.48		Gain of MoRF binding (P = 0.0089);Gain of MoRF binding (P = 0.0089);
MVP		0.56
MPC		0.78
ClinPred		0.040	T
GERP RS		1.4
Varity_R		0.020
gMVP		0.37

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-154293651;