rs1049305

Variant names:

• chr7-30924207-G-A
• rs1049305
• ENST00000441328.7:n.522G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-30924207-G-A
• chr7-30924207-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_198098.4(AQP1):​c.*578G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: AQP1 NM_198098.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 28 publications found

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 Gene-Disease associations (from GenCC):

• pulmonary arterial hypertension

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics, ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AQP1	NM_198098.4	c.*578G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000311813.11	NP_932766.1
AQP1	NM_001329872.2	c.*198G>A		3_prime_UTR_variant	Exon 5 of 5		NP_001316801.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AQP1	ENST00000311813.11	c.*578G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_198098.4	ENSP00000311165.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 790104 Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0 AN XY: 377662

African (AFR) AF: 0.00 AC: 0 AN: 16686

American (AMR) AF: 0.00 AC: 0 AN: 8806

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7608

East Asian (EAS) AF: 0.00 AC: 0 AN: 11186

South Asian (SAS) AF: 0.00 AC: 0 AN: 34686

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8638

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1750

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 672132

Other (OTH) AF: 0.00 AC: 0 AN: 28612

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.93
PhyloP100		-0.34

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

Other links and lift over

dbSNP: rs1049305; hg19: chr7-30963822;