NM_001170.3:c.406+2T>C

Variant names:

• chr9-33386402-A-G
• rs771895202
• NM_001170.3:c.406+2T>C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 6P and 2B. PVS1_Strong PM2 BP6_Moderate

The NM_001170.3(AQP7):​c.406+2T>C variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: AQP7 NM_001170.3 splice_donor, intron
• Scores: Splicing: ADA: 0.9998
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 9.04

Genes affected

AQP7 (HGNC:640): (aquaporin 7) This gene encodes a member of the aquaporin family of water-selective membrane channels. The encoded protein localizes to the plasma membrane and allows movement of water, glycerol and urea across cell membranes. This gene is highly expressed in the adipose tissue where the encoded protein facilitates efflux of glycerol. In the proximal straight tubules of kidney, the encoded protein is localized to the apical membrane and prevents excretion of glycerol into urine. The encoded protein is present in spermatids, as well as in the testicular and epididymal spermatozoa suggesting an important role in late spermatogenesis. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms. This gene is located adjacent to a related aquaporin gene on chromosome 9. Multiple pseudogenes of this gene have been identified. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.1341108 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 9-33386402-A-G is Benign according to our data. Variant chr9-33386402-A-G is described in ClinVar as [Benign]. Clinvar id is 402388.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AQP7	NM_001170.3	c.406+2T>C		splice_donor_variant, intron_variant	Intron 5 of 7	ENST00000297988.6	NP_001161.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AQP7	ENST00000297988.6	c.406+2T>C		splice_donor_variant, intron_variant	Intron 5 of 7	1	NM_001170.3	ENSP00000297988.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.0117 AC: 1853 AN: 158716 Hom.: 0 AF XY: 0.00903 AC XY: 802 AN XY: 88812

Gnomad AFR exome AF: 0.0101

Gnomad AMR exome AF: 0.00225

Gnomad ASJ exome AF: 0.00510

Gnomad EAS exome AF: 0.00497

Gnomad SAS exome AF: 0.00211

Gnomad FIN exome AF: 0.0282

Gnomad NFE exome AF: 0.0172

Gnomad OTH exome AF: 0.0104

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

Alfa AF: 0.224 Hom.: 0

ExAC AF: 0.0514 AC: 6230

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Uncertain	-0.010
CADD	Uncertain	25
DANN	Uncertain	0.98
Eigen	Pathogenic	0.99
Eigen_PC	Pathogenic	0.78
FATHMM_MKL	Pathogenic	0.99	D
GERP RS		4.4

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.84

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs771895202; hg19: chr9-33386400; COSMIC: COSV53004383; COSMIC: COSV53004383;