rs1004317

Variant names:

• chr7-30917243-A-G
• rs1004317
• NM_198098.4:c.385-4823A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-30917243-A-G
• chr7-30917243-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198098.4(AQP1):​c.385-4823A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,056 control chromosomes in the GnomAD database, including 23,252 homozygotes. 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: 𝑓 0.52 (23252 hom., cov: 32)
• Consequence: AQP1 NM_198098.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 6 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

ENSG00000250424 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AQP1	NM_198098.4	c.385-4823A>G		intron_variant	Intron 1 of 3	ENST00000311813.11	NP_932766.1
AQP1	NM_001329872.2	c.385-4823A>G		intron_variant	Intron 1 of 4		NP_001316801.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AQP1	ENST00000311813.11	c.385-4823A>G		intron_variant	Intron 1 of 3	1	NM_198098.4	ENSP00000311165.4
ENSG00000250424	ENST00000509504.2	c.922-4823A>G		intron_variant	Intron 8 of 10	5		ENSP00000421315.2

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78999 AN: 151938 Hom.: 23187 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.515

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.520 AC: 79120 AN: 152056 Hom.: 23252 Cov.: 32 AF XY: 0.521 AC XY: 38702 AN XY: 74330

African (AFR) AF: 0.819 AC: 33962 AN: 41472

American (AMR) AF: 0.415 AC: 6354 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1265 AN: 3472

East Asian (EAS) AF: 0.357 AC: 1845 AN: 5162

South Asian (SAS) AF: 0.554 AC: 2663 AN: 4806

European-Finnish (FIN) AF: 0.401 AC: 4240 AN: 10568

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26981 AN: 67962

Other (OTH) AF: 0.517 AC: 1092 AN: 2112

Alfa AF: 0.446 Hom.: 46397

Bravo AF: 0.530

Asia WGS AF: 0.475 AC: 1651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs1004317; hg19: chr7-30956858;