rs1004317

chr7-30917243-A-Gchr7-30917243-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
AQP1	NM_198098.4	c.385-4823A>G		intron_variant		ENST00000311813.11
AQP1	NM_001329872.2	c.385-4823A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AQP1	ENST00000311813.11	c.385-4823A>G		intron_variant		1	NM_198098.4	P1

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

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.517

Alfa AF: 0.434 Hom.: 15291

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

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

LitVar

Other links and lift over

dbSNP: rs1004317; hg19: chr7-30956858;